Been doing a lot of scouring of the internet to get this thing pinned down. Finally decided to post the problem as it hasn't seemed to be covered with my specific details.

Here is the lowdown;
99 xj sport 4.0 auto

I blew out the flexplate. In my haste to get the inoperable jeep off the road with a neighbors help towing I accidently turned the key too far (muscle memory and yeah I know face palm) and shot the starter into the now inoperable flexplate. Without my knowledge the starter must have stayed engage because it went on to burn my battery out. (another face palm) Fast forward to getting it back from the shop. It runs like crap now.

Rough idle; no power; almost sounded like it wanted to backfire; sputtering; would not go over 5 mph even when I gave it gas. Engine will not rev high rpms. I had it towed back to my place because the guy said he couldn't get to until two weeks from now. I need this back in action ASAP. (I think that was mechanic speak for I don't want to deal with your piece of crap.) I have not gotten any codes from it yet. The battery issue made the mechanic think that a scan wouldn't be helpful anyway because of the battery being freshly disconnected. I question this. I am going to get a scanner tomorrow to see what I find.

So here is the question. What would happen if the guy put the flexplate on 180 degrees out of phase? Or even 90 degrees out? would it have this effect? I do have a fresh cps I can throw on there to see if this helps the problem but thought I would get some input from the forum. Thanks.

 

it should only bolt up one way, the bolt pattern is not symmetrical. But if it's wrong (or the wrong part was installed), it'll mess with spark and fuel timing.
Your symptoms could point to weak fuel pressure too, might be worth checking.

 

I agree with methodical testing, but if you were spinning a trashed flexplate around it'd be worth the few minutes to see how damaged the crankshaft position sensor is.

 

I got under there and took the cps out and no damage. Went ahead and put the new one I had laying around in. Still impossible to keep idling. Also notice that while starting it the plate and starter aren't playing nice. Think the torque converter took the brunt and was bent during the maylay. If it is too far out of wack would this be a cause of super rough/barely there idle due to the cps not getting the proper info to the computer?

 

Yes.