From my experience there are two different shaft lengths, but that's not the problem from this thread. I got two PM102's (one for each jeep) and the shafts on those two were a little different. One went in with no problem and the other required a little shimming to make it work. Sounds to me like the quality control on these things isn't all that great and the tolarances on them leaves room for quite a bit of difference. As for the whole long shaft/ short shaft thing, the long shaft is supposed to be a LOT longer than the short shaft. Sounds like you guys are getting the right motor (you wouldn't be able to make the long shaft work with a few washers) but you are getting one with a little out-of-spec shaft on it. There's probably no real way to tell except to take your stock motor and measure several of the new ones until you get a match.
85 CJ7 258, borla header, Team Rush, MC2100 ,optima batt, Warn 8274, agr super box 2 & pump, T5 w/ B&M shifter, centerforce 2, superior 1 piece axles, warn hubs 2.5 in lift, 31" BFG MT
85 CJ7 258, A/C, T176, MC2100, Team Rush, Warn XD8000i, superwinch hubs, 3in lift 31" BFG AT/KO