Just seeing this thread. Being a former Bonne guy, I have the pinouts at the firewall mapped from 95 to 97, 98 and 99 if you wanted to pick up the harness, pcm and make yourself a couple of pin changes to have it work off the best pcm possible.
I'm assuming you are starting with an NA car. A 95 SC Bonne is a Series I motor, NA was Series II though.
Trans: The 4T65E benefit is that the pump was intended for higher rpm, the 4T60's had issues based on the pumps cavitating and starving the trans for fluid. Also many more of these have been built up than the 4T60. HD diff is considerably bigger as well IIRC. I would suggest going 98 or 99 as the TCC lockup etc is the better of the possibles and you could drop a 4T65E into it.
Suspension: Nice part of a Bonne is you can put in a set of drag bags for ~$80 and nearly kill all the weight transfer. This will make you faster off the line. You could also stuf a set of air struts in the back (SSEi or any of the bunch with autoleveling) and use the monroe airline kit (I think it's AK29) to help with more of the weight transfer by pumping up the struts as well. Neither of these items compromise ride quality. You could also swap up to the SSEi or PA sways/springs for slightly better cornering on the ocean with th boat.
Braking: if you want better braking, read up on 95NASTA's postings about his conversion to W body struts/knuckles and F body brakes. Bonne brakes are horrible stock.
Intercooler pumps and fuses/relays: Kinda cool depending on what you do, but you can easily add in relays and fuses to the center under the hood and have it look stock.
Motor movement: I can't suggest this highly enough and depending on what brand of headers you use, you likely will have to mod the mount anyhow for clearance. I removed the shock, cut the ear off and welded it horizontally. Used hockey pucks cut down as a spacer and a serious grade 8 bolt. (Password for all my PB is Boosted)
Motor Mount Photos by billboost37 | Photobucket
Exhaust: I went SLP headers into 3", with 3" cutout, then 3" high flow cat, 3" pipe from there straight back until the exhaust curves around the fuel tank. I left that piece 2.5" (stock) into a stock SSEi muffler with dual outlets. You shouldn't have any backpressure issues with that type of setup. And it gives you that initial throttle room in the 3" pipe. I didn't get the chance to use the cutout at the track.
If you go electric WP, consider adding the 2000+ Bonne power steering pump bracket. It moves the pump back about an inch or so and belt clearance to the TA mount is much better. (you'll need to grind that down as well)
Mezier Photos by billboost37 | Photobucket
Oil pan: When you get to pulling the motor. I highly recommend the 2000+ aluminum oil pan (Bonne), pick up tube and oil filter adapter. No more oil on the subframe and a structural pan that iwll allow you to jack the motor easily w/o pan issues when you change out the TA mount.
Intake: Depending on how you go.. it's super easy to spin you pcm sidewasy, pull the canister and retain it then use a nice big fwi
Want to go full IC with Gen V and N* TB. No worries about it hitting the hood. You are perfectly fine.
Thinking about upgrading your radiator from that thin poor excuse to a real one? Call RadiatorBarn.com and see if the 93 El Dorado with 4.3 they sell still has the 1 5/8" core. It's a direct swap in. Oh yeah!
Shall I keep going?
