Ever have a guitar that just won't....
If the guitar was tonally dead, I would agree with everyone else telling you to get rid of it. But you mentioned that it actually sounds good. In that case, you're just dealing with set up issues. Those can be easily dealt with.
It's really a shame that somebody took out the more attractive, solidly mounted, and traditional ABR bridge for one of those ugly and sloppy Nashville ones. Most people would do the opposite with a Gibson. The very slight amount of extra travel on a Nashville bridge is nowhere near worth the replacement. If a guitar is not intonating properly, a few millimeters of extra bridge width aren't going to matter. Tracking down the real problem will. And that problem is likely related to the nut and frets, as well as the set up.
In my experience, all new Gibsons need a new (or modified) nut and a fret dressing immediately after purchase. They simply do not do those things properly at the factory. Their nut slots are at the wrong height, cut at the wrong angle sometimes, and sometimes not even smooth. Their frets are not particularly well polished, not crowned very much (i.e. "boxy"), and very often not even level across the board. They don't properly dress the fret ends, leaving them boxy and sharp. The fret and nut work is pretty much EVERYTHING on a guitar...yet these are the things that Gibson is the worst at doing...because doing these things right takes a lot of time put in by a skilled specialist, and skilled specialist time is big money in a busy factory. Also, truly good intonation is impossible on most new Gibsons, due to their short scale length and inconsistent fret spacing in the higher register (1st-12th fret scale length is different than 12th-22nd fret scale length). Any decent tech should've corrected all of these issues (scale length issues aside) before doing something as extreme as drilling your beautiful guitar to convert to a different -and inferior - style of bridge. You can't do anything worth a **** with intonation - can't even judge it that well - until the guitar's nut and frets are properly tuned up.
In short, it doesn't sound like the thing ever truly got set up properly. By truly set up properly, I mean good nut and good frets before anything. It most certainly didn't happen in the Gibson factory, it most certainly didn't happen at the retailer, and it sounds like it probably didn't happen once you owned it either. You may have got a set up or two at some point, but I don't think they were very comprehensive or well done, based on what you're saying. If it was my guitar, I would have the nut replaced, the frets dressed, and realize that I had screwed up with the Nashville conversion and go back to the original bridge (yes, even with the required wood and finish work to do so). I'd also realize that the intonation on it can't really be "perfect."