I have now done this job on a 996 C2 and a 996 GT3.
Resign yourself to a long methodical process as you will need to do this very carefully and you cant afford to damage the cylinder heads. The job should be tackled in stages and it is worth buying some good quality tools to start with. Access to a good heat source such as Mapp gas or Oxy/accetaline set will also be a bonus. A Dremel or similar multi-tool with wafer thin cutting discs will be very useful along with 115mm angle grinder. And lastly a very good quality stud extractor will be your friend!(Sealey Drill Chuck Type worked best for me)
Don't under any circumstances try to use "easy out" reverse tap stud extractors because when they snap you will only be able to remove them by spark erosion - (way beyond DIY)
1. Bolts with a recogniseable head should be treated as a bonus because it may be possible to hammer on the next size smaller socket. It is best to use 6 sided Cro Mo impact wrench sockets as are less likely to remove the edges of the bolts.
2. If they wont shift with a socket and lever, heat them, then try to move them with an air or battery impact wrench. Heat them several times and repeat the cycle. If this fails the heads will probably round off or snap.
3. On Cat to Manifold bolts it may be possible to use a hacksaw and or Dremel and or angle grinder to cut off the nuts.
4. On the clamps that hold the Cat to Exhaust Boxes and Tail Pipes simply cut all the bolts off and lever open the clamps.
5. The most difficult part starts when the manifold bolts that are left, after trying all above, have nothing left to grip them by. The corrosion between the manifold and what remains of the bolt head means that the two are virtually fused together so the bolt head will have to be ground off using the angle grinder and/or dremel with mini cutting discs.
6. When all of the bolts or heads have been removed then it will be possible to separate the mainfold from the cylinder heads. In some cases it will be possible to grip the 5 - 10 mm of stud now sticking out from the head with your high quality stud extractor.
7. When this fails and all that is left is a piece bolt stuck in the head, the method of last recourse is to centre punch the stud and drill a small pilot hole thro the centre, taking great care not go too far and drill a hole into the waterway of the cylider head!!! To ensure the the hole is central AND at the right angle I re-attached the manifold and used it as a drill guide. Increase the size of the drill until you can just see the thread of the bolt. With a sharp spike it should now be possible to "implode" the bolt on itself and remove it.
8. If this fails, the thread in the head will have to be drilled out over size and a Helicoil fitted (a bit beyond DIY)
When you have gone through the pain of removing all of the rusted bolts treat yourself to a beer and new Stainless Steel fixings for the whole system using plenty of coppaslip assembly compound.
Link to Stainless supplier
http://www.a2stainless.co.uk/
Of course, if this all sounds too much like hard work, take it to your local OPC or Indy and pay them to do it!