The FI system is nothing to be scared of - it is one of the simplest electronic systems around. There are only a handful of sensors and switches hooked to the cake-pan sized analog brain. Quite dependable and works very well from my experience. Of course when it goes bad it isn't like tinkering with some carbs to get it back in tune - its more of an electrical gremlin mystery hunt. Here's a good site going over diagnostics:
http://www.icbm.org/erkson/ttt/engine/fuel_injection/d-jet.html
My own hint - check sensor readings by pulling the computer plug and reading across the porper contacts there - 1/2 the time the problem is in the wiring and not in the sensor. Checking at the plug checks both at once. If it is bad check again at the sensor itself to determine which is at fault.

1) As for a car that has been sitting for a while - it is possible (nay likely) for an injector to stick shut. The coils which open them aren't terriibly strong and gummed gas can overpower it. A quick test is to unfasten all 4 injectors (twist the sheetmetal collars that fasten them to the block) and pull off the entire array of wiring, fuel rail, and all 4 injectors. Then turn the key on and off several times to build pressure, and leave it on. Go under the hood and watch the injectors carefully while you pull the throttle open by hand. This will fire them in pairs. Look for any that dribble or drip when they don't fire, and look for all of them to have a nice healthy spritz when they do. If any are stuck and don't sprit you can try to free them by gently pushing in the pin at the tip - its the end of the valve. Once broken open again most injectors revive to resume long productive lives. Just run some cleaner through the tank.

2) Only repair/replace as necessary on the rest of the FI system.

3) Swap that tranny for a 4spd OD tranny and you'll love the car 76.5% more!:^)

4) Its a pretty decent possiblity that a caliper or two might have gotten sticky. It all depends on how huumid the storage area was and in the condition of the calipers to begin with. New calipers with new seals - no problem. Old calipers with dry rotted, shrunken, or cracked seals - problem. Also - the brake fluid absorbs moisture form the air and can rust the system from the inside. I'd flush the system by bleeding out all the old fluid until fresh clear fluid comes out all 6(?) bleed valves (2 on each front caliper - 1 on each rear). While you are doing this you could check for sticky calipers by pushing the brakes very firmly, then trying to turn each wheel as it is jacked up. (Chock it and release the handbrake for the rears!) Any dragging brake is cause for concern. Unfortunately there really isn't a cure other than putting new/rebuilt calipers on.