I have also heard the stories about FPE boxes catching fire. Good on you for getting them replaced. I can't really advise as to what is the best brand to use as the replacement, but I can address some of the other questions.
I don't think it's probably worth the cost to install a seperate service disconnect. You can work in a "live" panel with the main breaker switched off safely if you are careful; the only place that remains live is the terminals at the top of the main breaker. If you need to kill power totally for some reason, you can always just pull the meter outside.
On the grounding issue, if you're lucky, your house is already wired with a ground, and just has non-grounding outlets installed. If this is the case you can just install new outlets. More likely is that there is no ground conductor. No easy way to fix this apart from an extensive re-wire. I don't think it would be allowed to just run a new ground wire in the walls, I think you'd have to use new romex.
GFCI breakers are used to provide gound fault protection to an entire circuit, rather than the gfci outlets which can protect one(or more) outlets. They work by measuring the hot and neutral current (think of it as supply and return) and shutting off the power if there is more than a set difference (usually 10-20 mA). This prevents you from getting a shock to ground. You should have gfci protection in any potentially wet areas, such as outside outlets, kitchen and bathroom, basement and garage outlets. You could use a gfci breaker on the circuit to provide this protection, or install a gfci receptacle. The receptacle can provide protection for other devices downstream on the same circuit.