Replacing the rear quarters may seem very intimidating at first but once you "dig in " to the project it really isn't that bad, just time consuming. I've replaced both rear qtrs. on my '67 and my '69 along with many other pieces of sheet metal along the way. As far as tools go, it sounds you like you have a good base to start with but you should really consider a compressor as a purchase as it will prove invaluable to you. Also, you should invest in a spot weld cutter and quality 3/8" or 1/2" drill to drill out the spot welds. You are also going to need at least a hand held propane torch to melt out the old body solder where the sail meets the roof panel. If you don't intend on using a compressor and air cut-off tool, there are many electric cut-off tools out there and you will definately need one, a dremel tool will not hold up to cuting off a qtr. panel.
Another thing to take into account is what is the extent of the body rot on this vehicle? If the qtr. panel is rusted along the outer edge of the wheel opening, you may need to replace the outer wheel well. Not a difficult task but one you may want to keep in mind.
Other than that, I like to start by melting out the old body solder and taking it from there. The hardest areas to remove I find are where the qtr. joins the drip rail. Very hard spot welds to get at with anything but a cut-off tool and it takes a delicate touch not to cut through the bottom of the drip rail. Other than that most of the spot welds are fairly easy to get to. It is also alot easier if cut out the face of the qtr. so all the welds are easier to get at.