Runs like death

Ok so here it is. I recently went through a puddle that blew my motor and I went to the junkyard to buy new one. After installing the junkyard motor I got the Jeep started but it runs rough. It misfires and bucks then shuts off for about 20 minutes. I believe that it was the timing so I reset the timing and reinstalled the distributor. When I install the distributor I noticed that it would not one of with the number one post on the distributor cap its it's about a quarter inch behind. I know the distric annoying be installed one way so at this point I believe my timing chain might be stretched. Any thought or ideas on the subject would be so helpful. I have been at it for two weeks now. I live in san diego ca so if there are any xj pro's out there that would be awesome but any advise will help.

The distbutor can actually be installed way off if the the oil pump shaft is off. Best thing to do is get the the #1 cyl to TDC then get the rotor pointed right at it, may have to use a flat tip screwdriver to get the oil pump shaft pointed at it as well. Ive had this problem before. Have you put a timing light on it?

I have it set at 4°as per the book instructs. When i drop the distributer in in sits just behind the number 1 post and will not start. When i set it a tooth forward it starts but does what i discribed.

Better do what Jim says. Find TDC and go from there