It's a long story. Frankly speaking, there are pretty much just as many things you can do to a Series 1 as you can a Series 2, but some are more difficult than others. The bottom line is that with the age of the car, there are certain things we've learned the hard way that MUST be done first, or you'll end up with huge repair bills. The biggest is to start planning for your transmission right now, and have at least $2500 in the budget for that, sooner is better than later.
The rest of your questions might be answered here:
http://www.pontiacbonnevilleclub.com/fo ... m.php?f=44
Several of the articles there will apply to your car. I suggest the following:
1. Full tuneup and diagnostics FIRST. I'm sure someone will chime in with the full list.
2. INTENSE FWI (fenderwell intake), buy the 1997 Bonneville kit and relocate your charcoal canister.
3. Series 2 (1997 and newer) L67 ignition coils (OR MSD).
4. High-flow catalytic converter. Keep the stock resonator and muffler for the time being. The muffler will only affect sound, not performance.
5. Remove exhaust manifolds and take them to a shop that can weld the cracks. This includes removing the 3 heat shields and fixing cracks under them. They ARE cracked, all of them do, but when properly repaired, are the best-flowing EM's GM ever produced.
6. Buy a scantool that can read KR.
7. (last):
http://www.pontiacbonnevilleclub.com/fo ... =44&t=1660
8. After that, you can do 1.8 ratio rockers if you like.
I will caution you that you're opening a big can of worms on a car this old. You will likely end up causing more problems than you think along the way. I've learned that the hard way with both of mine.