I just finished a frame swap on a '97 back in May... I had the same issue, I was putting a 4 cylinder frame under a 6 cylinder jeep.
I cut the engine mounts off both frames, being careful to not cut into the new frame, and being sure to not ruin the 6 cylinder mounts...
They have to be located very carefully when you go to weld them back in. Also, the mount for the steering shaft will have to be cut off and moved. I used the steering shaft and bracket off the old frame and located and welded it to the new frame. The bracket that is on the 4 cyl frame will be in the way of the 6 cyl engine mounts.
When I did my swap, I lifted the engine, transmission, transfer case, and driveshaft off the old frame together... then when I went to locate the engine mounts on the new frame, I bolted them to the engine, set the entire assembly in place, connected the driveshaft, and bolted the trans mount to the skid... then set the engine and mounts down onto the frame. This allowed me to use the drivetrain as a 'fixture' to locate the mounts. I tacked the mounts, unbolted the engine, trans mount and driveshaft, then lifted the drivetrain back out so I would have room to fully weld the mounts in...