As you probably know, cylinders 1 & 4 use a common coil in the coil pack and fire simultaneously. Assuming your sensors are ok and properly gaped (I read somewhere else that crank sensor gap problem can cause a pair of cylinders to not fire), maybe there is a problem in the coil pack which caused a secondary failure in your power train control module driving your coil pack - and the replacement power train control module that you put in also got blown. Try resistance testing your coil pack. See the following link which is not for an LHS but an Intrepid - but might be useful in testing the coil pack. I'm not sure if the pin outs or resistance measurements are the same - but you get the idea.
http://www.dodgeintrepid.net/showthread.php?t=176259 Also, make sure the spark plug wires for cylinders 1 and 4 are ok and not shorting out.
There seems to be something else that does not make sense. If you are getting a good spark on 4 of the 6 cylinders and fuel and timing were ok - I think you would expect to hear the car firing on the 4 cylinders - and maybe, start and run very rough. Do you hear any of the cylinders fire ok - you said it does not start? Did you change the timing belt- and are you sure it was properly aligned? I also assume you checked compression after the rebuild and is now ok on all cylinders.
A couple of other things to check. Make sure your wiring harness is good (continuity)between the power train control module output connector side connector and the coil pack input connector side of the harness for the 1&4 coil control signal wire. Also test for fault codes. There are relatively inexpensive code readers available.