When doing anything with the cam belt, you need to make sure the cam pulleys are properly located when buttoning things back up. You use 3 1/8" diameter pins to locate the pulleys and keep them from rotating out of position while doing whatever you need to do. The good news here is that the X wedge is a non interference engine, so no worries about valves hitting pistons. So you might start with verifying your cam timing is correct before pursuing other avenues.
You have an S&S X wedge service manual, yes? If not they are on the MTWC website in the 5 speeder section, or pretty easy to find (free) just via Google search.
The pins are 3/16 not 1/8
