The pivot bracket on the front of the tunnel was cut out, it got in the way and I didn't need it. I went with a Lokar universal shift rod that works perfect with the OE shifter. You can see pics of it in this thread.
I'm not sure on the motor mounts, I reworked my own. But you could try loosening the mount bolts a bit where they mount to the frame rail then wiggle til it fits.
On my project note, I'm going with shock extensions up front to get some shock travel back and relocating the rear shock mounts on the diff for the same reason.
My plans changed a bit on the rear shaft. To use my current shaft I would have to drop my trans mount, crossmember and rework all the various shift linkage as well as dropping some coin into a new ignition system. The reason is it dosen't drop enough and if the rear would hand, it's most likely the tailshaft of the t-case would break. In dropping the t-case, it would put my HEI in the firewall meaning I would need a smaller set up. My new plan is getting a c/v-double cardon shaft built for a slip yoke t-case. I would be money ahead since it would eventually be needed anyway if I decide to lift if more.