1. I've got autometer gauges and about the only thing I would change is to get the ones with the chrome ring around them rather than the solid black that I have. A nice thin chrome ring gives a definate "vintage" appearance.
2. Don or DV could tell ya!
3. What I did at a great number of spots (i.e. where ever I needed a ground) was to drill and tap a #10 hole into the frame (or larger, up to 1/4" for the headlights). Use a Dremel motor tool to scrape/grind away the paint from the hole. Solder a ring lug on the end of the ground wire, cover the solder joint with heat shrink tubing. Screw (#10) or bolt (1/4") the ground lead to the frame. Cover with a thin layer of dielectric grease. (Come to think of it I've probably got a good 10 feet of heat shrink tubing in my Cobra ... heat shrink cut to 1/2" lengths and used on the end of wires!)
4. I prefer the rubber hoses simply because they are cheap and I know they will work well (some engineer and some lawyer at Ford made sure the hoses are good enough for street use)!
5. I haven't had a problem with the stock brakes yet. The only problem I could imagine is overheating the brakes during autocross. Larger discs will give you more leverage (the calipers are mounted further away from the center point of rotation so the lever arm is longer). My wife would like a stronger booster in the brakes but then again she's half my size!
6. I don't know. Flex plate? Whatzat and how does it work when there is a flywheel in the way!