Stock front brakes with rear disk conversion in the back. Rear brakes have some spotty areas with rust and an imprint of the brake pads from sitting on my driveway for a couple months before I did the swap. How do I know if its the front or rear rotors that need attention?

 

you warped a rotor, to play it safe you might have to replace them all.

 

sounds exactly like my scenario awhile back
replaced the rotors and solved the problem

 

before you go replacing rotors
go for a drive
beat the **** out of your brakes, that may eat up the rust and make the shaking go away

you may also have a thing called film transfer,

go beat on ur brakes, and tell me if that helped at all