2.8L to 3.5L engine swap in cherokee

[grinch]

My little bro blew up his 2.8 liter engine in his cheorkee. I have heard the 93 commaro 3.8 liter was a bolt for bolt swap pritty much for a auto tranny. Here is the dilemma he has the stock manual transmission. Does anybody know if this conversion will work with the Manual tranny? If so what needs to be modified to fit it in?
Thanks for the help we need it