My question is about the holes left in the intake runners after having my heads CnC machine ported. Do I have to cut the bolts from the rocker arms shorter and what is the correct procedure to seal the threads from leakage?

 

You don't have to cut the bolts, but if you want to get every last bit out of your setup, you should. If you cut them to make them flush with the top of the intake wall, then you'll have to keep track of which bolt went into which hole. You won't be able to mismatch them after you cut them. I did this by numbering each bolt and each bolt hole on the head. I just used my dremel. Also, make sure to torque them down exactly the same amount each time to ensure that they are in the head properly. The torque spec is 22 foot pounds, so make sure to base everything off of that. Otherwise they won't be exactly flush. I used blue locktite to seal the bolts and it's worked fine.

By the way, welcome!