Does it matter where I put the ground on the coil portion? There are 3 nuts that hold the coil assembly down, does it matter which one of those I use? I used the top one, the one closest to the fender, then ran a wire from there to my negative post on my battery.

 

The trailing coil grounds through the ignitor to the body. There is no need to run wires to the battery.

If you are really worried about it, remove the attachment bolts and thoroughly clean the bolts and threads of rust then apply dielectric grease and reinstall.

 

Well I did that too, took the coils off the ignitor and used a wire wheel on a dremil to clean it all off and make it nice and shiny and cleaned off the bolts that hold the coils to the ignitor. I basically attempted to clean all metal to metal surfaces.

 

That's good. You won't get any better of a connection by running a wire to the battery. It will just clutter up the engine bay.

 

If you really want to make sure the cleaning made a good ground take an ohm meter and test the resistance from the coil casing to the negative batt. terminal. If it is well grounded it should have like .2 ohms (not to be confused with .2 K ohms) or some outragously low number.