First, if this engine is over say 30-40K miles, you should be inspecting the valves in the heads ANYWAY, so this doesn't apply. This only applies to engines with low enough mileage and evidence of good maintenance that you can reasonably expect it to run well without disassembly. This will only be a small percentage because some junk yards will leave their engines sitting outside so water/dirt can get into passages. Those low miles motors that the junk yard pulls and seals up in a warehouse, these are the ones you could have some faith in.
I'm going to just spell this out now because so many people have been asking me how-to. I don't normally like how-to's because it locks in peoples way of thinking and I'm not interested in mind control. lol But take this for what its worth and be creative in your own right. If a person needs more of a how-to after this one, then they are too retarded or lack enough creativity to work on this project!

This how-to assumes that he engine is drained of fluids, intake manifolds stripped, exterior accessories are stripped and it is mounted on a stand so you can turn the engine.
1. Pull valve covers and remove the cams and chains, make sure to mark every cam cap, timing chain direction and orientation with a white-out pen. Also look for the white timing marks on the chains, clean them and remark them so you won't miss them later.
2. without sealants, reinstall the timing cover and valve covers and tighten the bolts reasonably, but not full torque, just enough to compress the gaskets.
3. Tape off all vent tubes.
4. Tape off with masking tape or duct tape the front crank seal entrance, or reinstall the damper just enough so it mates to the seal around the crank, push it on by hand to close the gap.
5. Tape off the coolant passages on the block and heads, Tape off the spark plug ports on the valve covers, tape off the crankcase vent if removed from the valley or the end if not removed. Basically, any miscellaneous hole leading into the engine must be taped off.
6. Take paper shop towels, wad up enough of a towel to make it a plug and push it down into each intake valve runner, one per valve. Cramm it in tight.
7. When all 12 valves have a wad of paper towel tightly plugging them off, take grease and reach in with your finger and coat the wall right around where the paper towel touches the wall. Make it a somewhat small, narrow bead around the towel.
8. Take your lower intake manifold gasket and cut the bottom alignment tabs off. Set it in place with the bolt holes aligned.
9. Carefully take a black sharpie pen and trace a perfect pattern around the ovalport with a line thickness equal to the pen tip thickness (about 1/8"), noting where the old injector feed area is that must be filled.
10. With a cutting bit, rough out the shape of the port to the tracing, stop with about half the black line remaining (about 1/16").
11. Shape the entrance to the ovalport area to make a smooth transition from the rounded ports to the lower portion. Get at least a good inch and a half down into the port but don't leave any ridges.
12. Shape a nes injector feed port that widens out like a fan, similar to the old port area so that the spray can travel outward. Refer to old 2.5L heads if necessary.
13. Clean out the ports by using a shop vac and sucking out the aluminum, Don't go too close to the towel and pull it up right now or you'll have to clean it all out and repack them.
14. Next, use some solvent on a rag and clean the old, center mounted injector port.
15. Take masking tape and stick it to the port area where it sticks all along the bottom and leaves a pouch open at the top. Creating a sort of kanga roo pouch.
16. Mix up some metal/epoxy weld of your choice, I used JB Qwik and it's working awesome for mine so far. Pour it into the pouch up to the level of the gasket surface. You will of course had to have made a substantial enough pouch to create vane in the airflow, tapering down. This matches up to the gasket when the gasket is put on and should be tapered at the top. Don't worry, you have 5 minutes to reshape it as it cures.
17. Make sure you put in just enough where it isn't lower than the sealing surface but not too high or you'll be spending time triming it down.
18. After about too minutes it is thickening up nicely into play dough consistency. Don't put your finger in it. start squeezing the tape with your fingers to make the vane shape that will match the gasket. Eyeball it but don't worry you can trim it easy enough. Get it to where they all look good and consistent. Continue to observe until you have a somewhat hard plastic vane and you can just dent the top edge of the epoxy with your finger nail.
19. Okay while it is still workable, pull off the tape and check your vane shape. At this point just use a razor to trim anything. Don't worry about down in the port. At the top, shave with the razor across the top until the epoxy is level with the aluminum sealing surface.
20. Let it cure for a few hours, or until hard and sandable. Could be overnight will work best.
21. Take a small sanding drum on a die grinder and sand out the ports and now you can sand the edge of the epoxy vane. Use a small dremel to completely smooth out the injector feed port you made. Make all of them look alike with the gasket sitting on top. Note how much overlap the lower intake has on the gasket and make sure that the lower is port matched to the upper at this time.
22. Vacuum out everything with your shop vac.
22.5 --- If at this time you want to touch up the exhaust ports for a bit more size and flow, do it now! Leave the paper towels in the inake while you are at it. You don't want metal flakes flying around again once you do final cleaning.
23. Pull the paper towels out carefully. Vacuum again.
24. Turn the engine upside down, lean under with safety goggles and spray up into the ports to flush out anything. Spray out with compressed air, or let dry. Take a hose and hose out the ports with water, use a small brush to knock around each valve. You'll get wet but water is heavier than solvent and you have a whole hose stream of it.
When satisfied, flip it sideways and blow out all the water with compressed air or let drain and dry upside down.
25. Make sure you sweep your work area and blow it out with air to get all loose particles out of the way before you rinse out the engine.
That's it, you guys should be able to knock this stuff out in your sleep now. My only fear is that cheap skates (cheaper than me) will start slapping in tired/worn out engines in and make things even worse, or fail to do this properly and cleanly and cause some more problems.