when you put the studs in all the way, should they all be sticking up the same distance? i started to put mine in and they are all about 1/8 - 3/16 off from eachother. They wont go in any more.
Yes, they should all be the same. The factory does not drill different lengths into the block and all the bolts should be the same length to begin with. I am guessing the threads in the block have the lock tight gunk in them preventing you from turning the stud all the way until it seats. Buy a chaser and clean the threads out. You can also put oil on the threads to make sure you dont strip them while doing this.
I re-used the factory studs because they have the middle flange on the stud that stops it when it makes contact with the outside of the head. Also, you can tighten the stud on the end using a small mm wrench or socket.