Here are all the links I have been able to find for this topic. Some are better than others. Hope this helps any and all who are currently doing this swap.
new title: 2.5 -> 4.0 swap - Your project MJs - Comanche Club Forums
1986 cherokee 4.0 swap - JeepsUnlimited.com Forums
2.5 to 4.0 motor swap on comanche - Jeep Cherokee Forum
2.5 to 4.0 swap - MJ Tech - Comanche Club Forums
4.0 Into An '86 - MJ Tech - Comanche Club Forums
4.0 Swap ? - MJ Tech - Comanche Club Forums
4.0 swap into 2.5 comanche....how much fun? - Jeepin.com Forums
86' 2.5 to 87' 4.0 swap? - MJ Tech - Comanche Club Forums
86 mj - Your project MJs - Comanche Club Forums
BIG Swap Help - MJ Tech - Comanche Club Forums
Dash removal - Jeep Cherokee Forum
Dash Swap In An '86 Mj - MJ Tech - Comanche Club Forums
Need Some Clarification On Some Things...
Oh, and my build thread which is a slow progression of this topic:
http://comancheclub.com/topic/39492-the-truely-custom-86-mj-custom/?do=findComment&comment=397509
http://www.cherokeeforum.com/f46/86-comanche-dd-159524/index4/#post2542580