Well.... number one, no you cannot just slap on the Eaton M62 onto your engine. Everything is different, let me give you a short list...
1) Intake manifold is different (supercharger instead of runners)
2) Heads are different to accomodate for the supercharger vs. intake manifold
3) Injectors are in a different place since the supercharger moves them to the heads for the */C version of our engines and ours are in the intake manifold.
4) Tranmission is different, the supercharged engines get the -HD or heavy duty which can handle the torque that the Eaton dishes out at very low Rpm'* (like 2k).
That'* just for starters. But there are things you can do. Depending on how much you want to spend you can...
Do an intake, make your own or buy one made for a ricer that is the same length, it'* going to be a short ram intake, cold air ones are tough to make. Secondly you can do exhaust and uncap that since the American companies and GM like to cap power through exhaust size. Those are simple mods. I am not too knowledgeable on your 88 Bonny SE...
Do you want more radical ideas or more simpler ones to make your drive around town more enjoyable? One thing to do is check your bushings on your swaybars, if you havent changed them then they are trashed after years of being on your car. And Addco makes swaybars for your year of Bonneville.
That is the link for the swaybars. So just let me know if you want more crazy ideas or more simpler ideas to work with and I am sure me and many others can help you out here. I hope this helps and good luck with your car.