Hey, Doc! Bill rebuilt his Regal'* suspension after some intense preparation. If you're looking for inspiration, have a look here.
Aluminum only corrodes at the outermost layer, and that helps insulate the inner layers from further corrosion. For an excellent and high-tech look, definitely get anodized if it'* in your budget! Aluminum is tough to paint well, especially for an undercarriage, in my opinion. I have trouble painting aluminum in general...
For steel and such, you probably have POR15 as a solid option. I have some on my car, and it is fantastic. I'd recommend painting everything first and then putting it together. Then, do touch-up work if you don't mind the occasional interruption on your surfaces. Let us know if the bolts hold their paint, but your best bet with them is probably going to be to get stainless steel ones instead. Black paint on top of those put on in the touch-up process should help hide their shine from the black underside.
Please take plenty of pictures!