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


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