You could always get tumbler and try maybe ceramic or graded stone media to clean them, then switch to walnut shells and a little polish to clean them up.
You could also try dipping them in rust release, I never used the stuff but my boss restored an old jeepster and he used it for some really bad parts and said it worked good. Could maybe try the rust release and an ultrasonic together.
Lincolndieselspecialties.com carries most of all the bolts you need on their website at a pretty decent price.