the battery doesn't seem to drain while left alone and connected still

I did intake gasket on 3.8l 1999 windstar, I hooked up the battery it wasn't able to start the van but had some power left i boosted it let it run then it died out and was like battery was dead? lights came on stronger but still couldn't start it again till boosted. is there an issue with the pcm where it needs to be reset? i removed the wiper cowel where the pcm is. could I have done something there? the battery doesnt seem to drain while left alone and connected still just when I start the van via jumper cables it runs till no more juice to run components i checked everything that I disco'd till i found out the pcm is located under cowel would that also be the cause? the battery and charging system was fine before the intake was removed but I cant seem to see anything wrong, im not sure if its the alt. or bat. i remove battery cable while van is running and the van dies instantly. but i have found a TSB regarding something like this but not quite. not sure if i need to get an alt or battery or have the pcm reset????

Answer:

The problem is not likely the PCM the problem is more likely the alternator or a wiring connector was left off the alternator.