I also ran into this problem. Prothane did not ship directions. I left out the factory shim plates also. The only problem it created is the exhaust is about 3/8 inch from the motor mount and that was after much adjusting of the pipe. So I wrapped the pipe in header wrap and hope it does not get too hot. The shims would give me another 1/4 to 3/8 I suppose.
One other thing, the gold anodized plates molded into the mounts need to point up. I did not know this and pointed them down. Later found a picture on prothane website with them pointing up. I wish they would have included some basic instructions
1985 CJ7, 258, TF999, D300, D30, AMC20, 4.5" lift, 33" BFG's