I refinished the top of my SEX Amp a few years ago after I was unhappy with the original paint job.
Some items can be slightly loosened to improve the re-finish job. For example, the IEC cord socket can be lifted up a little so the paint gets to the edges of its cutout, RCA's can be loosened and lifted for the same reason, on/off switch, etc. In other words, things that have flanges or other features that would be hard to mask and might trap a contrasting color under the edge might be worth just lifting a smidge to paint.
The transformer is easy to mask, so not much sense disturbing it to paint, so long as painted fastener heads don't bug you. If you don't want them painted, you can use some RTV silicon to cover them if you're careful not to get any on the surface you want to paint. Tube sockets, given the other things ganged on their fasteners, are best left in place and simply masked, I think.
If you want a stained base after having coated it with a clear finish, it might be easier to fabricate a new base. Sanding through the clear all over can be a challenge and getting into the rabbet cut recess for the top plate would be difficult. If I were doing it, I'd keep the poly-coated one to make a solid colored base and fab a new one for staining.
Good luck!
