Gutting my coupe... how far?

I'm not a body expert at all, but I think you will want to get the 'body' assembly manual. It lists all the dimensions for all the critical area's.
Also, make sure you are on a FLAT,LEVEL surface, and all your jack points are even.
Some things to think about...

you are going to want to brace the unibody befre you start cutting. ive used the rear window regulator attaching points, along with the lower door hinge mount. get a piece of 1" tubing and a piece of 3/4" allthread with nuts.with one nut welded onto the tubing, it makes a dandy screw jack that can be used with a couple pieces of angle to move the unibody around after it is cut apart.you can also tack weld tubing to the sheetmetal, but once it is welded in you cant move things without cutting...

What will be the end result of the work? Restoration? Show car? Track car? Drag Car?

For the most part I'd say take off one piece at a time that way you'll have the old piece (even if it's going to come off later) to line things up with. I've saw magazine articles of bodymen changing both quarter panels and the tailight panel all at once and that's ok if you have the experience. When I did it I put on one quarter panel at a time and then changed the tailight panel last. That way I had something to line the pieces up with.

If the floor is very bad I'd go ahead and buy the complete floor panel. I've never done one but you'd have to brace the body up real good before cutting the old one out.

When you do the cowl I'd recommend drilling several holes around the outside all the way through all panels. I've never heard anybody say to do this but when you put the cap back on you can align the whole thing up with these holes. You can just drop a bolt or something through these holes while you weld it up. After you have it back on you can weld these holes up.

It is best to get your car sandblasted to see the problem spot, and based on the extent decide whether to replace whole panel or not. I would not replace shock towers unless I absolutely had to. keep in mind that replacing a panel is usually more difficult than patching it with sheet metal

Cowl area is another problematic spot. The only way to replace it is to drill out about 200 spot welds. An option is to completely remove cowl area and install air intake for fan/heating somewhere from engine compartment, + instal some decorative (watersealed) mesh.