I have a 2000 Intrepid that came with a 2.7, I bought it with a blown motor. I did the 3.5 HO conversion on the car. It ran great until latley. when I start the car in the morning the check engine light will come on, after I drive it for a couple minutes the check engine light will start flashing and the car has reduced power. I have checked the codes and the are as follows:
#6 Injector, #6 Cylinder and Circuit Malfuntion.
Some times it will also say Mas air flow and air volume, not sure on the last one but I think I have it correct.

Anyway the car will run rough and miss until it reaches operating tempature and then it runs fine,as long as the car does not cool off it will run great all day, in fact the check engine light will go out after a few time of starting it.

But if I leave it set and the motor cools down it will miss and the check engine light come back on until it's up to temp again.

Any ideas?
I have another Intrepid that was rolled and has the 3.5 conversion done to it also so I can swap parts if needed.

There's a few here on this site who have done that swap, but you may want to try over here:

http://www.dodgeintrepid.net/

or use the search feature about swaps. I know there were a couple of threads over there.

I hate to be captain obvious here ... but since you have spare parts ... did you change injector #6 and or look at the wiring for it ?

Stop driving it with the check engine light blinking. On obd2 cars this means that you've got a misfire bad enough to damage the cat. The reason the power is decreasing besides the misfire is that you're cat is overheating and plugging. If you get the codes I can look up the diagnostic trees for you, and possibly give you an idea where to look.

I installed all new injectors when I put the motor in, along with the timing belt and water pump.
The codes are as I said, no numbers, I have one of those little Mac tools that read the codes and can clear them, It's about twice the size of a key fob. I have smelled something hot so that must be the converter.

How are you checking codes? On my old 3.5 swap the codes the ODO read back after the key dance were different than the ones that showed up on my basic Actron Scanner.

Kinda sounds like you may have a vacuum leak either in the intake or plenum around the number 6 runner. Try spraying with some carb cleaner when cold to see if you can pinpoint it. could be leaking till seal warms up and swells to seal.