PB blaster works great on the exhaust studs/bolts. If you have a weepy valve cover though, you may find several of the bolts are fairly easy to take off.
The smoke isn't gasket sealer. It's manufacturing byproducts, residues if you will (or any crap you might have gotten on your header while installing) burning off your header. It's perfectly normal and will stop quickly.
You don't need to apply a thick layer of the gasket maker. If the bolts come loose it's not going to "fill in" the holes. The purpose of it is to help the two different surfaces conform to one another when you assemble. It's job is to fill in super tiny holes and imperfections in the surfaces. Copper spray helps you apply a thin even layer over the surface. If you can apply a thin uniform layer of copper by hand then go for it.
Reusing the stock hardware is also absolutely fine. If you can clean them up well and the threads and heads aren't damaged there is nothing wrong with reusing them. They aren't at too high of a torque value for their size, and are not put under terrible stress.
Loctite is not necessary either. The joint is designed well and has more than enough bolt stretch in it to not need any type of thread locker. You'll be hard pressed to clean thread locker out of the threads in your head if you do have to remove and reinstall your header multiple times.
If you reuse all the stock parts you can use a little bit of anti-sieze on the threads if you like, but you don't have to.
I don't know about the brass bolts there...the bolt stretch will come easily with the brass, but the bolt itself won't be under as much tension since it's so much softer. You might want to use loctite if you go gonzo and stick brass in your block.
As well torque values are usually calculater from the fastener. Depends on size, threads, material, etc. If you're changing material your changing that equation so the torque number won't work out the same. Like I said before, just don't mess with the brass. -I'm all for it though on the collector-mid-pipe connection. I'd probably just use stainless, but brass would work too. Don't worry about the torque there, just crank the heck out of it.
later,
Nick