The swap is a walk in the park overall. The motor uses the same block.
The fuel system is totally different though. You will need a Series 2 L67 (SC'd) fuel rail and injectors.
The throttle body on the S3 is drive by wire. You'll need a TB adapter and a throttle body. Depending on your future plans, I'd recommend either a stock L67 TB or a LS1/Northstar (2000+ Caddy 4.6 motor) with LQ4 (Chevy truck) maf.
Swap all your brackets onto it and lightly modifiy the evap vacuum routing.
Use either your exhaust manifolds or headers on for exhaust.
Change the oil filter adapter from a W body that heads for the passenger ide tire over to the H body that tucks under the oil pan. Might as well add an oil pressure increase kit while you have it apart.
Once you have it mostly done, you'll have a clearance issue with your alternator. You can clearnance the alt by shaving the back side of it slightly or swapping it to a different style. (Been there..done both). The different style requires a different connector...if you can solder well, it'll be seamless.
And then there is the consideration of your transmission. Currently your trans is the non-HD 4T60 transmission. This area is probably one where if you plan on modding (which it appears you will) that you need to consider many options. More on that later.
As for wiring, there'* no need to change your harness. You can add an extender for the MAP sensor and add the wiring for the boost control soleniod. Both Intense-Racing and ZZP sell a conversion kit.
PCM... You would proably want to source a 96 SSEi pcm. As for tuning the only options are GMTuners.com or a DHP Powrtuner. This should also be considered in talking about the transmission.
Trans/PCM considerations. You have the non-HD 4T60 transmission. This is the wimply version of the vacuum controlled, heat producer transmission that in HD form is known for differential issues. It is relatively easy to move up to a 4T65HD transmission, the fully electronic, slightly beefier and cooler running transmission that became available in 97. Pretty much to do it, you swap the trans, add a different connector, add 5 wires to the pcm connector and change your pcm to a 97 SSEi. (You guessed it...I've done too much).
Holler if you would like some pics of things etc.
00 Regal GS: All kinds of cool stuff.