The only varnish I would worry about removing is any that kept the back screws (with the solder tabs) from making contact with the choke/OT frame. That is remove any varnish from the inside of the mounting holes. The frames are grounded through those screws to the solder tabs attached to the ground bus. Be sure to keep those shoulder washers to isolate the frames from the plate. You only want the one ground point for each. The same goes for painting the frames, just scrape off any paint inside the mounting holes.
I have the full nickel transformers in mine and love the amp. Enjoy!
Also I want to point out for folks reading this that as far as I know, the Magnequest transformers aren't available for the current 2.1 version of the amp. I have the 2.0 version.