Having a similar problem (possibly exactly the same) with a WJ stroker from a 99 Grand Cherokee I'm trying (AAAAAAHHHH!) to put into my 2000 Wrangler replacing my TJ that threw a rod. It was a great price, $400, but I'm freaking out because of all the issues.
I've got the engine in but my buddy noticed a space irregularity in the mounts. I will need to chain lift the engine again to adjust the motor mounts, which looks like your (thanks Upjohn!) suggestion might work out.
But then as components were going back in, I found a missing post for the alternator and no post for the ac condenser. As I struggle forward I'm wondering if pulling the engine back out and selling it to get the proper fitting motor in is the solution, or if I should fabricate some brackets. I have (till my cuz gets sick of me taking up his precious lift) the use of a full shop with metal fabrication and welding capacities. Any thoughts would be appreciated. One step forward, two steps back...