First pick up some PB'laster penetrating spray at any auto parts store. It's alot better than WD40. I actually found mine at Wal Mart. Soak the bolts REALY good every day for at least 2 or 3 days for maximum effectiveness. They aren't impossible to get off, but are definitely a PITA if things are really rusted. Make sure to use good fitting quality tools, and DO NOT use any 12 point sockets or wrenches, since avoiding rounding off the bolts in the first place is the most important in making it a tolerable job. I had good luck hammering a 1/2 in open end wrench (or socket, depending on which nut it was) on the badly stuck ones. It's slightly smaller than the 13mm, and the super tight fit will usually guarantee that the wrench will probably break before the bolt rounds off...and I didn't actually break any wrenches when I did it. Just work slowly when it starts comming loose. If it binds, just work it back and forth, soaking in penetratring oil to help loosen the rust on the threads. Don't just crank it out, or you'll be sorry. This is especially important if the stud is the first thing to loosen since you don't want to tear out the threads in the head. You just need a lot of patience and nowhere to go for a day. When I did mine, the studs weren't stuck at all in the head, although some of the nuts were rusted pretty good to the studs. The real nightmare is the y-pipe flange bolts, since they are really hard to get to, especially if you need to cut them off. Mine were absolutely miserable, since they were practically welded into the headers with rust, but I have the old cast headers and I only sprayed them down with PB once and it only sat one night. I ended up twisting most of the bolt heads off and having to drill/dremel the remains out.
It would be a good idea to just replace the studs and nuts while it's apart, and use lots of anti-seize compound at re-assembly.
Exhaust work sucks...and which way do the manifold gaskets go?
You'll probably be able to gain a little more clearance to remove/install the headers by gently jacking the engine up to relieve pressure from the engine mounts. Another 1/2 inch would definitely help.
At least for removing the stock headers, I've found that just removing the 1-4 header from both the head and the y-pipe allows the entire exhaust system with the 2-3 header still attatched to be removed. This will make tackling the y-pipe bolts on the 2-3 header much easier. This reqires enough clearance under the car for it to work, but a good set of jackstands, or in my case, some drive up ramp stands under the rear with a floor jack under the front crossmember would work fine.