Okay that makes more sense to me now. Part of the reason I was confused was your use of the term "tranny tunnel". To me the tunnel is the hump running down the middle of the body to clear the transmission and driveline.
I'm guessing you installed the typical 1" spacers between the crossmember and the body, but from the pictures it looks like maybe more? I'm thinking the easiest fix is to lower the bracket that's on the body. Get a square piece of 1/8 or 3/16 metal and drill holes for the original mounting screws at the top, a new set of holes 1" lower to mount the original smaller plate, and a hole for the shaft to stick through.
You might be able to redrill a hole higher up on the bracket thats attached to the tranny as well. Pop out the plastic bushing and measure the original hole. I don't think that bracket will bend up very easily as I think you were suggesting. It's bolted to the aluminum flange where the xfer case.