Wow, helluva 1st post!
So, first... welcome to the board! Don't feel like wanting a Subaru for non-performance-first reasons makes you less of a "Subaru Enthusiast", these things are unbeatable in the AWD grocery getter role, and a 2.2 Wagon is a great car for the job.
Since I'm not one of the "old schoolers" (I've only owned a WRX, the RS guys will know more about your vehicle than I) I will only be able to gloss over your list a bit, so keep that in mind.
A. Wheels & Tires ---
Alloys will be stronger and lighter than steelies. That means a little bit more acceleration, and a little better fuel mileage, as well as a little bit less of a chance of off-road failure. 16" WRX takeoffs are readily available, usually in the $300 for a set range. You will end up running a lower profile tire on the 16" rims, so that might reduce the car's off-road ability. Plus 16" tires are more expensive. Honestly, the best be would be some 15" alloys, but I can't think of anything short of expensive rally rims for a Subaru in 15".
B. Suspension ---
Again there are WRX takeoffs, but you'll need to swap the rear strut mounts as the GD mounts don't fit in older Imprezas. The WRX struts would be stiffer but not a lot... they'd increase the handling potential of the car on tarmac without losing very much off road capability. The next step would be STi takeoffs, or full coilovers, since pretty much all the other spring/strut combos are for lowering and stiffening.
C. Interior --- currently beige
1. WRX seats are pretty nice. Lots of side bolstering. I' not quite satisfied with the lumbar support, but I'm 6'4", so I'm the special case. I believe they bolt right in. Only thing to note, the WRX seats have integrated airbags... you won't be able to hook them up, so you might want to remove them... I don't know the procedure to safely remove them.
2. A short shifter probably wouldn't make a big difference for you. IT doesn't sound like you're racing or anything where the extra feedback and faster shifts would be important. Plus the short shifter bushings would just make more noise in the cockpit.
3. Already have a CD player
4. Extra gauges ---
You can get AutoMeter electric gauges for Oil Temp/Press and Trans Temp fairly cheaply. I figured out a way to convert an oil cooler bypass adapter into an oil temp/press gallery, so that's not hard. I'm not sure where the tranny temp probe would go though... it might have to go in the drain plug, which, as you mentioned, is in a vulnerable location. However, I don't thing a tranny temp gauge for a 5MT is that necessary. A better water temp gauge or a voltmeter might be more useful.
D. Exterior --- that forest green color
1. Has a luggage rack
2. You can us the existing locations in the bumper for a set of Hella rally style lights. The Hella 500's are just slightly larger than OEM Subaru fog lights and w/ minor work will bolth in there. The also sell 4 light patterns for the Hella 500s: fog, driving, cornering (I think) and pencil. The fog pattern lights up the ground down low, the driving is a middle pattern, the cornering light light up the sides and the pencil beam is very narrow and lights up objects very far away. I've got a set of Hella 500 driving lights to replace my factory fogs. $70 for the pair, and they're brighter than god!
Note these lights (except the fogs) will pretty much blind all oncoming traffic... I've got mine wired to only come on w/ my high beams.
3. I think the '98-'01 2.5RS hoods are bolt on to your car. They'll give you a very v3/4 STi wagon look!
Green will be hard to find.
Steve got one on his Green L though... if he decides to sell his L, you might be able to trade him!
4. "Rally" lights on the front? Has this been done? -- see #2.. and there are plenty of options for light bars to hold additional lights!
E. Engine --- 2.2l
1. Reflashes probably won't help your car. The real benefit comes on the turbos where you can increase boost. On your car just concentrate on getting air in and out of the motor faster... that means intake and exhaust... which means noise...
2. Turbos and Superchargers are expensive... in addition to the compressor itself, you need engine management, fuel delivery upgrades, inter/after cooling (potentially), and probably a bunch of custom piping. It's been done, but it's not cheap... and IIRC the 2.2L is a bad platform for forced induction... runs like a champ unmolested, blowes up easy when you start boosting.
F. I doubt a LSD is worth it on you car for your purpose. Hell, the unit itself pretty much blows your budget, let alone the cost of installation.
G. I'm not sure what it takes to convert drums to rotors. I'll be that WRX brakes would fit on the front though... but there go your 15" rims!
Like I said... I'm just glossing over this all... I'm sure we'll all have more ideas over time. Try coming out to a meet! With the car in front of us, I'm sure we'll all have a ton of great ideas to spend your money on!