If the SF bolts are in good shape, I'd reuse them.
re: manifold studs, I bought Josh's Stainless Steel studs for $30 (listed under Performance) and used brass nuts with them. Don't use the supplied SS nuts or they might gall on the studs.
You could also make your own studs using whatever bolts or studs you can find at a hardware store. To remove them, you'll want to heat them up and put 2 nuts on the stud. One nut will act as a jam nut to lock the other nut in place. Use a wrench to carefully rotate the stud out of the manifold using the non jam nut. If you break a stud, this can easily turn into a huge problem.
Ian