So I was putting in my head studs and noticed that some go in further than others. Some have a few threads showing. The instructions say to go hand tight. How far should they thread in and how tight should they be?

Hmm, I'm not quite sure I understand the question. Hand tight until they are all in and then they'll need to be torqued in the correct sequence and to the current torque spec.

Edit: now I see, studs not bolts. Are there instructions to follow, pretty sure you still need to tighten the studs to a minimum spec, likely by locking two nuts together or if the studs had a hex end, which a lot do. You may also want to use a tap and chase the threads in the block to confirm they are all clean and the depth is the same.

Thanks for the advise Kirk and Phil. I'll tap those tonight and clean them out.