1: Accoring to NAPA, Subaru had 2 different clutches available for 1993. One was pre 06/1993 and the other was after 06/93. In searching for a performance clutch and flywheel, I haven't found any mention of this difference. What are the differences and are they interchangable?

2: Are there any tranny swaps/upgrades that don't require replacing the rear diff? If not, what would be my best option? I plan on Autocrossing this summer. (=abuse;))

I believe it is the number of splines on the transmission shaft. So the plate would not be interchangable. One of the tags on the car, I forget which, probably inside the door, has the month and year of manufacture.
You can use an Excedy pressure plate for any EJ series up to about 2001 (check the exact year).
You don't really need a performance clutch with the power the 1.8 puts out the stock tranny will be fine. I would just put in a performance gear oil, there are a lot of differences of opinion on what is better there.

My car is pre-6/93.
I am more concerenedwith what will happen when I do an engine swap. I will probably go with a 2.5L, so it would need to be stout enough.

With the pre 6/93 your options are somewhat limited. You can find a heavy duty clutch but I don't think there is much available as far as discs.
You could get a OEM disc, send it out to a performance clutch builder, and have a better material riveted on.
When you swap in your engine, you could do the transmission and diff too. A limited slip might be nice for auto cross with the extra power from the 2.5.
Look for a RS wreck.

Would the 2.5 tranny swap be plug and play? Any wiring that I need to research? I understand that the rear diff will need to be changed, what about the rear CV's?