So, I currently have my engine completely tore down, cases split, crank, trans, everything broken down. Just need to heat up my cases to get the bearings out. Sorry babe, I'm using the oven.

What I'm stuck on is removing the head studs, or as the Clymer manual states; crankcase studs. I've been in this engine quite a bit in the 2 years I've owned the bike and this is the second time I've had the cases split. When I bought the bike the output shaft to the trans was all chewed up and so were the splines on the pulley so I had to replace that pulley and the output shaft.

Back to the question of concern, do I need to replace the head studs? I assume those studs stretch over time with me loosening and retorquing them. Do you think it would be best to remove those after I heat the cases up? I figure they are going to need heat  to be loosened but I definitely don't want to go and heat up just those areas with a torch.

I'm replacing all the bearings and nuts and bolts while I have the engine broken down to this point. I plan on doing some power upgrades.. cough cough cam and piston and carb.. cough.. so I figure why not freshen up everything while I'm in there. I'm not trying to rush this and throw it back together. If it takes me a year to get it done, it takes me a year. I want it to last and I sure as heck don't want to split the cases again for a while.

Any help would be appreciated. Thanks!

Bike is a 1996 Savage. I ride her hard but never put her away wet. She's my baby.

Unless your head nuts were grossly overtightened, the studs aren't gonna be any longer.  The stud has to be stressed past the material's yield strength to "stretch" it to the point of permanent deformation.  You mentioned that you have had it apart before.  If you were able to achieve the specified torque reading on the first reassembly, and you didn't exceed specified torque, I suspect your studs are just fine.

BTW, I have removed those studs several times.  Never had a problem using the double-nut method.  They come right out.  No heat required.  However, if you are working on a beater that has endured years of water intrusion down the right-rear stud hole, that could be a problem.