Get some heavy grease. Such as axle grease, or really any kind you have available. Squirt a bunch of it in where the pilot bearing is. Take a rounded (cylinder) shaped piece of metal, or maybe a wood dowel will work. Stick it in the hole in the bearing and if its full of grease, hit the end of the dowel with a hammer. It should pop the bearing out slightly. Then pull it out and refill it with grease. The heavier the grease, the better off you will be. Eventually after doing that enough, it will pop the bearing out.
The throw out bearing it really easy to get off. Held in with two clips like the other guy said.
As far as installing an aluminum flywheel, its no harder than getting your old one resurfaced and installing that. I dont remember what the specs to torq it to are, but read in the manual. If you get a fidanza one you'll need to figure out if you're getting a 10.5 or 11" clutch and then align the little metal pins onto the flywheel accordingly. It makes sense when you actually do it. THen bolt it up and call it a day.
If you need help, feel free to Instant message me at BoostedStang302 on AIM