This is my first build of this magnitude. First time using milodon gear drive. (Still don't quite understand) . Thought I had it. When I did the clay neither valve touched. Also wasn't quite getting valve lift on intake according to cam card. It wasn't until I put all together prime and rotate that I run into problems.
Those gear drives can be tricky to setup. There are no dots like a chain to get you in the ballpark. Your comment that you had clearance the first time is telling.
Re study the instructions on how to setup the drive. Make sure you understand how to do it. When you get it right you may be ok for clearance.
Here's a link for you to read on the milodon drive setup. Installing a Milodon Gear Drive on a Big Block Chevy - OnAllCylinders
