Ah, well, coulda' been worse.... I was contemplating making a neck-through V-type until I saw what you've been through. I may just hand it over to someone else for finishing if I go ahead with it.

About the control pots: If you go with the long-shaft versions, get some extra nuts and washers for them. Position the extra hardware on the threaded portion of the shaft to control the amount of shaft that stands proud of the guitar top. Leave just enough protrusion to install the final nut and washer on the top. The knobs will then mount as close as possible to the surface.

The SG body would probably not be thick enough to permit this solution. The long pots would require too much depth behind the mounting surface.

For that guitar, the only way would be to route the control cavity deep enough to leave the wood 3 mm thick around the mounting holes. This is probably an acceptable approach for the CS335 as well. A cutter with a ball-bearing tip would keep you centred on the hole, although the carved profile of the top makes setting the router depth tricky.

If you have enough room for the long-shaft pots, I think that's your best bet.