Super 6....can't put it off any longer. manifold questions

Refer to this article and this thread.

Yes, there is some risk that you might break off a stud if you go to remove and replace them all, but figure it this way: those studs go through thousands of thermal cycles. That causes metal fatigue. If a stud is about to break, you have a choice: do you want it to break as you're tightening the nut while installing the manifolds (thus necessitating complete re-disassembly and doing the entire backbreaking job all over again)? Or would you rather have it break with the manifolds off the engine so you can get right to work removing the broken-off stub and not lose time undoing the manifold install only to have to do it again? There's only one right answer to this question.

Besides, removing all the studs gives you a chance to fix that hamfisted "repair" (a bolt is not appropriate as a replacement for a stud here; that's begging for problems down the road—this does not bode well for whatever other work was done by whoever decided to take the slackaѕѕed lazy way out instead of correctly replacing the broken stud) and you can also take the opportunity to make sure each new stud has appropriate thread sealant on its cylinder head end so as not to have to deal with coolant leaks later on.

The rest of the studs dont have much thread showing

When you buy new ones, make sure to get the correct length.

meaning I wont have much room for a thick gasket.

Fix it (correct-length studs) so that you will, or you are setting yourself up for frustration and aggravation. The Remflex gaskets are enough much better to be worth doing whatever is necessary to get your setup back in correct shape to accept them. That goes for both the manifold-to-head gasket and the intake-to-exhaust gasket (the stamped sheetmetal type in the Fel-Pro kit almost never seals fully).

Please give any advice for the removal process

Thread two of the stud nuts onto one stud. Jam the nuts together with two wrenches. Then put a wrench on the nut that is closest to the head and pull—don't jerk, but pull smoothly—with your wrench.