Jeep Strokers

I made this engine swap a few days ago. (2001 Wrangler TJ Sahara) It started first turn off the key. Ran it for the 20 minute cam break in and shut it off to do a little clean up. Started it up again (it started a little harder) drove it to the corner and back and it ran smooth but a little rough when it came down to idle for a few seconds. The next morning it had to turn over 6-8 ties before it started. Drove it a mile down the road and back. When I came down to idle it was running very rough for about 10 seconds and then smoothed out. Backed in the garage, turned it off and it hasn't started since. I have fuel pressure at the fuel rail and you can hear the fuel pump for a second when turning the key on. I'm not getting gas into the throttle body while cranking. I put a shot of starter fluid directly into the throttle body (a no-no I know) with no results. It seemed like no spark at all. I replaced the MAP Sensor. The battery has been disconnected several times for 30 minutes plus. All plugins have been checked and double checked. The place I got the engine Golen Engine Service) says the computer doesn't need to be reprogramed. Some of the jeep guys say the 2001 is not a learning computer and will retain the factory settings and won't deal well with the changes. I'm getting a little frustrated. I can fix a problem like this on old 283 or 327 with points. Fuel, air and spark and your running but this computer stuff is way beyond me.

Can anyone help me out here or tell me where to go? (LOL)

whatever happened? Did you get trouble codes? Sounds like you need to index the CPS

Any luck?