Welcome to the forum!
As far as mods go, even though you don't have to worry about the plastic intake (you have a pretty Eaton M90 instead), I'd still do the 180° Thermostat FIRST. Yes, even in winter. Come spring, ADD a tranny cooler. From there you can get a custom Series 2 intake from www.angryducktofuracing.com
he'* the only one currently manufacturing intakes specifically for the Bonneville. He'* also working on exhaust as we speak, including headers. Those are the 3 big mods. Thermostat/cooler, intake, exhuast. From there you can go with a smaller supercharger pulley, chip, brakes, or anything else under the covers you like. There'* tons of potential in these engines! You'll find out very quickly that the tires are going to be the weak point. Do a couple mods and you'll see what I mean!
Be sure to check out the Techinfo section. There'* a link on the Header bar above!