Hey guys. Ok I just put my motor back together in my 94 mustang cobra. Its has a lot of modifications. I tore it down to check my cam out and replace the headgaskets. I realised that the timing gears had the option to advance/retard the cam timing after I had already taken it off. So when I put it back on I set it to stock specs.After putting the motor back together I drove it down the road and it stalls out on me coming to a stop. Not all the time, but a lot of the time. I cleaned the maf, Iac, and the intake air temperature sensor. Ignition timing is good. Set to 10 degrees base timing. No vac leaks. Everything is the same as it was before except for the cam timing(as far as I know). Does anyone have any idea why this could be happening? Its very irritating. Plus I don't know if the car was tuned for a specific setup or not.

Replace the Ignition Control Module. It's simple and cheap to do on your Mustang.

I got full msd ignition and just put in a brand new distributor and coil

The worst ignition problem I every had (by far) was with a MSD ignition. I refused to believe it was causing my car to regularly die in traffic. I tried everything to no avail. When I removed their ignition, everything was fine and no more problems. You will likely be pretty much on your own in this matter.

Is your ECT Sensor working properly or is it flooding the engine?

Well I hope its not my ignition, it was working perfect before. But yea it could be flooding the engine, because I have a wideband a/f ratio gauge hooked up and it seems to run very rich at 1/4 throttle and above. And when it stalls out its always after I give it more that half throttle, right afterwards the engine will just shut right off. I thought it was dumping a bunch of fuel in there and drowning it out. But I don't know how to check for that.

They are inexpensive and easy to change out. They contain a thermistor, where the resistance should drop as the temperature goes up. You can attach a DMM and see if voltage appears to be changing with temperature. Corrosion, due to not changing the antifreeze frequently enough, is the major reason they act up.