Pulled 4.0 out of daughters 96 cherokee to replace oil pump and timing chain. Had my son (good mechanic) and son in law (learning) for help. Son pulled transmission linkage off trans to get it out of the way. I think son in law reinstalled. Sometimes it works great, other times acts like its starting in third gear. What could we have gotten wrong? I am a heavy equipment tech by trade but never fiddled with a jeep auto. Thanks in advance

 

Try adjusting the throttle-body to transmission cable.

Otherwise check the fluid level, and that nothing is messed up with the shifter linkage.