Those replacing the clutch in manual transmissions have removed them regularly, since the Y-pipe needs to come down to get the trans out. Those with auto transmissions have to get them out for a rebuild, too.
If the engine were in, your best bet would using a long 20-24" extension (so you can lie down on the ground without having to sit up in an uncomfortable position, and so you have the full range of motion away from the Y-pipe and transmission) and a breaker bar/flex handle to pop them loose, then a long handle ratchet for enough leverage to keep up the torque when loosening them. I've never used anything other than 3/8" tools to get them out, I think using 1/2" tools would be overkill and you might break the bolt off rather than break it loose.
With the engine out, you can probably just use a breaker bar and socket while standing in the engine bay.
I'd highly suggest squirting some spray penetrant like PB Blaster on the threads from the top so it makes it's way in there. Putting it on every few hours over a period of days before doing the job can make busting them loose a lot easier. You should also squirt a little on as you go, and work the bolts loose rather than just go at it. Turn them back clockwise after you get a turn or even half a turn. Once they come out a bit, spray the penetrant on the threads from that side, then turn them back in, loosen, spray more penetrant on, and repeat. You might also want to take breaks and let the bolt/manifold cool down, if you just work a bolt back and forth too long, it will be very hot from all the friction, and that can help it break off as well.
I've been able to get them out every time, the first time was the hardest since they seem to lose a little material each time they come out. If they are too badly rusted or the threads are damaged, you can get new replacements from Ford. You can also use regular hex head bolts with the same thread pitch, but I prefer using washer head bolts, since they really help when re-installing the Y-pipe. Regular hex bolts, even with loose washers, don't really cut it. You also really need to use the same class (grade)bolts here, not just low-grade cheap stuff.
You should be able to replace the manifold gaskets without having to remove the manifolds from the Y-pipe. If you're thinking there is some kind of gasket between the manifold and Y-pipe, there isn't. It's a metal-to-metal press-fit circular flange seal, and the rust and crud seals it up airtight. The only other gasket besides the manifold-to-block gaskets is the oval gasket between the Y-pipe and the catalytic converter.