If you mean you can't reach the nut, a 1/4" socket set and a few u-joints will work. if the nut won't tighten up to the head, There may be a piece of the old stud broken off in the hole, keeping the stud from seating fully into the head. There's an unthreaded section that will keep the nut from going more than halfway down.
Getting a broken off section of stud out of the hole is not going to be easy. A set of washers may help bridge the gap, but if a stud broke out of the hole, the threads at the outer end may not hold. But, I'd definitely try that first, lol.
Yes, you can get the head and header off as a piece; you'll want to read up on the issues of removing a head in the car; It's not easy, but there are a couple of things that make it easier. The only one I remember is that you have to pull the bolts up, but they won't come out; there was something about a rubber band to hold them up. Search, you'll find it. disconnecting the header from the exhaust will let you pull it out, with some wiggling. Don't forget to unplug the o2 sensor, you don't want to ruin the wiring.
This might be a nice time for upgrades; you could find a crown vic or gran Marquis in the jy and grab the heads and intake.

Hell, if you're unbolting the head...