Do some searching & reading, get the swap manual from Advance Adapters. People have been swapping 350's into CJ's for *decades* so there's plenty of info out there. The LT1 is a little more complicated from a wiring standpoint but there are enough resources out there since 350 swaps into just about anything are pretty common that you can easily find places that'll setup your harness for you, burn custom ROM's, etc.
'86 CJ-7 Laredo: 4.2,T-999,D300,D30/D44,'94 YJ tub, full cage, Shrockworks rockers, OYR corners, AC,cruise,restored seats,3 tops,2.5" Superlift,F-T shackle reversal, RS9000x's,35" Dunlop Mud Rovers.
'83 Scrambler: time & money pit under construction with parts from CJ's,YJ's,TJ's,FSJ's,GM,Ford,IH,Honda,Toyota and a whole lotta aftermarket & custom stuff.