97 Jeep Cherokee XJ Code 11 "Timing to far advanced"

First off a little history before I explain the situation. I have a 97 XJ with a stroked 4.0 in it(4.6). Its got a slightly larger cam and ford 24lb injectors in it. The computer and everything else is stock. Its been in the jeep now for almost 9 years and has been flawless, it has about 50,000 miles on it. However I have had a problem with it kicking back on the starter ever since I put this motor in. I have checked lots of stuff with no luck, I just deal with it and put starters on it more often than I should have to. Its NEVER had a check engine light.

A few weeks ago I had to put a new distributor in because the shaft bushings were smoked in the old one and it was making noise. I put a brand new non reman distributor in. I originally just tried to swap it and out jacked up the install and it didn't want to run right. I then set it at TDC and re stabbed the distributor according to internet info I found lol. Now, it doesn't kick back on the starter and it hasn't ever since I changed the distributor. It runs perfect but it has a check engine light on about %80 of the time and a code 11, the codes go 12, 11, 55 and thats all that is there. Sometimes it will start and have no CEL and when it does this it lopes for a second then idles and runs perfect. If it starts up with a CEL it goes right to idle with no problem. I find it weird that it says that the timing is to far advanced but it no longer kicks back on the starter? Any ideas?

Thanks for any information