Well I would start off with the lower compression pistons, and for your low HP goals you could put stock TT pistons in there. You will also need bigger injectors. You could use stock TT size but I would probably step up to the 555cc. Then you will need to have a custom tuned ECU, which shouldnt be a big deal since there are a good number of people out there doing that now. I would also look into either getting an aftermarket fuel pump or getting a stock TT unit(which would be more than enough). Thats about the bare minimum that I would do(that I can think of off the top of my head).
I guess since you are converting it to a track car then you will be getting rid of the AC so you should have the space for your supercharger. Making up a bracket isnt too big of a deal.
As for what you can get rid of.....As you said the EGR, you can get rid of all the water lines under the intake plenum, since you have a 90 you can get rid of the AIV system. You need to do alot of searching through twinturbo.net to get more info, they have about anything you need to know about a Z32 on there.
**My Opinion** - If you are going to go custom then go big. 380HP is hardly worth your time and effort. Put forged internals in the engine and get yourself a P1SC at the least. I would think you would be good for 600rwhp. Also, doing something just to be different when it comes to cars is rarely a good idea. Most times its different for a reason, because most people found a better way to do it.