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Ok, I have an update. BTW: DavidZ, I used new gaskets, but I have had the upper IM off like 10 times since then. I keep checking the gaskets and there appear to be no issues. I will consider changing them if the exhaust work has no effect. I also think I'd need to be leaking a serious amount of air to effect the stuttering that I have felt.
As a test, I pulled my new exhaust off and put the stock exhaust back on. I reset everything and checked how it ran. The stuttering was reduced but not gone. The rpm point at which it goes away has dropped now to a lower rpm, about 2800-3K now. It is more driveable now at low rpm, but has some surges. This experiment plus the data from the dyno has me all screwed up. At the dyno I was able to put down about 202-203 wHP with the new exhaust, even with the stuttering in effect. Peak torque has risen to about 194 Ft-lbs. At low rpm it looks like PA3L's first dyno run, but then it smooths out about 4K rpm. On the AF curve, we were able to use the GReddy to drop it to about 12.5 to 13:1 in the low rpm area, which is certainly good enough to run on considering that my last dyno was showing 14.5:1 and no stuttering. Since the AF is good, and the high RPM is good, I have to propose another hypothesis. I am thinking that it could be a turbulence issue caused by my gutted pre-cats. With the newer 2.5" exhaust, I think that I have a lower exhaust velocity until I reach high RPM. At low velocity, the turbulence in the pre-cat chambers could be going back into neighboring cylinders and causing them not to expel all of the exhaust, and causing a misfire on the next stroke. As velocity goes up, more exhaust would be moving in the proper direction and there would be less chance for turbulence to reverse its direction into the cylinders, and therefore it would not misfire. If this is the case, there may be some critical exhaust velocity that is needed to overcome the effects of this turbulence. The 4 facts that I shared above agree with this hypothesis. 1. Bigger more open exhaust means lower exhaust velocity, and I had more stuttering and it extended higher into the rpm range although it still went away with the IMRC opening. 2. Smaller stock exhaust is more restrictive and would increase the velocity in the lower RPM ranges, therefore you wouldn't need as high of an rpm to achieve this so-called critical velocity. 3. The problem goes away completely with the IMRC opening, which would mean almost twice the intake volume, and therefore more volume of exhaust. This greater volume must increase in velocity in order for it to exit the cylinders in the allowed time. More pressure would also build up so that the effects of turbulence would be minimized due to the higher velocity and pressure (although power is lost). 4. The RPM at which the stuttering has gone away has lowered with respect to the smaller exhaust system, possibly indicating that the smaller exhaust has increased the velocity.
As to why the system doesn't do it when cold: The manifolds are not heated to the extreme temperatures yet so the exhuast would be cooler initialy. Cooler exhaust will take up less volume and is less energetic overall. Manifolds that are at high temp should cause the gasses not to cool as quickly and would continue to cause the rapid expansion.
Ok, that is long but I needed to provide all of the information so that you people can pick it apart if possible, or offer up some alternative ideas. BTW: Would all of you professional automotive engineers that are on this board chime in on this topic, and on my hypothesis?
warmonger
You can call me anything you like as long as it's nice.(all lies accepted) 99 Silver Frost SVT. #226 of 2760 Engine: 3.0 power! Unique Stuff: Sunroof control module (#1 of 9) Car Audio: Loaded and loud! Check them out at http://home.earthlink.net/~twilson1726
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Awesome News!!
For me at least. After analyzing all the data and posting the above post, I tried to devise a new test that would either prove or disprove my theory. Well, the overall idea is that there is turbulence in the exhaust, and that the higher the exhaust velocity the less of an effect the turbulence would have. Also, when the secondary's opened up it would always go away. This is an increase in the intake charge which means more exhuast, which in turn means that the exhaust velocity has to go up to get rid of the exhuast assuming the pipes are the same diameter.
Well, I figured that by wiring the secondaries open I could increase the airflow. So I went out about 20 minutes ago and tried it. The stutter seemed gone! I was able to do a 5th gear pull from 1500 rpm without the slightest surge or stutter.
Apparently there is a small stutter right about 1000rpm now, but it is gone by 1500rpm.
This is all in agreement with my theory in the above post.
It was very simple to try this test. I took some wire and after removing the air intake boot I could see the spring assembly where the imrc is actuated by a cable. I just took some wire and tied it to the throttle cable brack to keep them open. I advise those of you with the stuttering problem to try this test. Just because you haven't gutted your pre-cats, you may have some turbulence caused by clogging in the pre-cats. Not all people may be affected by this, but if you have the problem when the engine is warmed up, but not when completely cold, then try it as the temperature of the manifold can greatly affect the exhaust flow characteristics.
The end result should be that a good set of headers will cure the problem.
warmonger
You can call me anything you like as long as it's nice.(all lies accepted) 99 Silver Frost SVT. #226 of 2760 Engine: 3.0 power! Unique Stuff: Sunroof control module (#1 of 9) Car Audio: Loaded and loud! Check them out at http://home.earthlink.net/~twilson1726
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Ok here is a question: What if we just cut out the enlarged cat part and weld in a stainless pipe so the air would be less turbulent?
I don't like the MSDS header option because everyone has had issues with rust. Minnesota is not going to be forgiving on them. I wish we would have a stainless steal option cheaper then a grand.
Later, Chris
1999 V6 MTX Black Cougar
Jacobs ignition system, Borla dual exhaust, Sho shop y pipe and hi flow cat, gutted precats with MIL eliminators, IAT rewire, vitek ignition wires, SCA CAI with monster flow filter, Unorthodox racing pulley, BAT rear strut brace, Battery relocation to trunk, eibachs, KVR crossdrilled/slotted rotors, freedom design strut brace and Tuned S-AFC
Waiting to be installed: svt engine with 11k miles on it/ fidanza flywheel/Quaife/energy suspension engine mount inserts.
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Weapon-R will be coming out with SS headers shortly that will fit the Cougar. Since the engines are the same, they will fit the Contour and 3.0 since the ports/bolts are all the same 
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Ok some news:
I had my car looked at and the coil pack was fried, the wires were fried, and the car has been running extremely rich for a while so there is lots of carbon in the engine.
Solution:
He replaced the coil pack and wires and took off my cold air intake. He put the MAF right up to the throttle body with some hosing and the car runs fantastic. He said it feels like a completely different car. It has tons of low end power. NO MISFIRES AT ALL OR STUTTERING!!!!
He is still working on the cause so wait until tomorrow for an update.
Later, Chris
1999 V6 MTX Black Cougar
Jacobs ignition system, Borla dual exhaust, Sho shop y pipe and hi flow cat, gutted precats with MIL eliminators, IAT rewire, vitek ignition wires, SCA CAI with monster flow filter, Unorthodox racing pulley, BAT rear strut brace, Battery relocation to trunk, eibachs, KVR crossdrilled/slotted rotors, freedom design strut brace and Tuned S-AFC
Waiting to be installed: svt engine with 11k miles on it/ fidanza flywheel/Quaife/energy suspension engine mount inserts.
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It doesn't sound like we have the same problem. I swapped coil packs with the stuff from the 3L engine as well as checked them all with an ohm-meter and nothing was wrong. Of course I have driven my car all day with no stuttering with the secondaries tied open. Good for you though.
warmonger
You can call me anything you like as long as it's nice.(all lies accepted) 99 Silver Frost SVT. #226 of 2760 Engine: 3.0 power! Unique Stuff: Sunroof control module (#1 of 9) Car Audio: Loaded and loud! Check them out at http://home.earthlink.net/~twilson1726
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BlackCoog - Congrats on what the mechanic says. I anxiously await you confirming this, though, through your own driving the vehicle. I dont want to sound skeptical, but with this problem.... you know the story =] If it is solved, your about to have a new life of ownership =-). Hey Warmonger, I also saw what you posted and I was curious as to what you meant by having no stuttering with the secondaries tied open. Do you mean after all this, you can eliminate the stuttering simply by having the secondaries open all the time - or was this on the 2.5, etc etc. Just curious about your statement. Thanks guys.
BlackPantherSVT 2000 Contour SVT Black with Midnight leather #2075 of 2150 Mods: K&N drop-N Champion double-platinum plugz "Mystery Mod" Resonator replaced: Glasspack
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Originally posted by warmonger: Of course I have driven my car all day with no stuttering with the secondaries tied open.
warmonger ...and that isn't a big enough hint to yank them... :p Sounds like a weak IMRC. Pull the IMRC plug, clean it and reinstall it with dielectric grease. If the problem still exists your motor is most likely on it's way out. Just pull them and gain mad power... 
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Brad Noon '99 SE MTX 3 point oh my God H.O. 179HP/178TQ BNMotorsports Floormats, powder coating, TB optimizing, Gutted cats, etc BNMotorsports is now the preferred distributor of Contour/SVT/Mystique Indiglo style gauges!!!bnmotorsports@msn.com
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No, I checked the whole IMRC setup. Besides, it runs great once the IMRC is activated and the power goes up. Below the point that it opens is the issue. With the IMRC pinned open now the stuttering is completely gone. As far as gaining power down low with them tied open, I notice no increase. I will have to put those headers on to see if there is an improvement though. If turbulence is indeed the issue, then I wont be able to tell any benefits until it is gone.
If the headers eliminate the stuttering, then I will do new dyno tests that with everything equal except the secondaries either pinned open or closed. I suspect there will be no increase in torque with them pinned open, except around the opening point. I will let the dyno determine that. BlackPantherSVT: Please try to tie open your secondaries. Yesterday is the first time I ever tied them open. And yes, with them tied open the stuttering is essentially gone! That may be a hint to remove them for someone with a stock system, but not for me. I won't remove them until the dyno tests show an improvement, and that will have to wait until I have made the vehicle operate well with everything hooked up properly. Anyway, please take some wire and tie the spring-loaded lever to the open position and then test drive it. NO need to reset anything. I pulled my intake boot from the throttle body to gain easier visual and physical access, as well as the pcv valve. It took 5 minutes to use a piece of wire to tie them open. Please let me know ASAP if this test (with everything else stock) works for you.
warmonger
You can call me anything you like as long as it's nice.(all lies accepted) 99 Silver Frost SVT. #226 of 2760 Engine: 3.0 power! Unique Stuff: Sunroof control module (#1 of 9) Car Audio: Loaded and loud! Check them out at http://home.earthlink.net/~twilson1726
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