No start, has spark, has fuel, only when warm? anyone?

Here's the scoop. Changed engine due to two broken and ceased (or pressed in manifold studs. Motor ran fine. After the engine change, it started immediately and ran very smoothly. What I have discovered is that if I let it warm up and shut it down, when I try to restart it, it only cranks and will not fire. I checked for spark at the end of a high lead and have spark and there is plenty of fuel pressure in the rail. I also discovered that if I mash the gas to the floor, it will fire up although under a flooded condition. (Black smoke out the pipe and it must be revved to blow out the extra fuel.) My gut feeling is that there is a problem with the injector and/or spark timing - things are getting there but not when they need to be) and this is only when warm. From what I can understand, there are two ways of delivering spark in these cars (module mode and some other way). I think the other way (CDImode or something) kicks in after the car is warm. Anyone have any suggestions? Does anyone know how to find out what are sensors are used and when they are referenced? This car seems to be an electronic nightmare! Thanks.