I've tried a few different lighter strings previously. I decided to try a heavier gauge set to rule that out, as well (Thomastik-Infeld flatwound .013-.053). Unfortunately, this didn't help the ping either.
That harsh metallic overtone is exactly what I hear also on my guitar. It's not as noticeable when amplified. But I play unplugged most of the time, so I'm still trying to figure it out.
The frets on my acoustic are about the same size as the ones on the 1996, maybe slightly bigger/taller. I spent a lot of time getting a good, pretty low action on that guitar. Maybe I should lower the bridge on the 1996. (It should be easier to play than an acoustic.) If I could avoid out-and-out fret buzz, it would probably just as easy to play as the acoustic.
If this "ping" overtone were present only on the open, non-fretted string, I'd say that the nut slot would have to be refined (proper slope). In my case, I think it's my failure to fret properly. Sometimes you just can't fret all strings properly at once -- I do not have any crooked finger joints at all, and for, say, a cowboy "A" chord I have to use three fingertips; not really that easy on a little Rick fretboard if you're really moving along with your tune, compared, say, to a big Fender neck.
One last (final?) option would be to deliberately change the tuning on that one troublesome string -- either decrease or decrease the pitch of the open string when you tune up. You'd have to experiment in both directions. See what it sounds like. I doubt some minor off-key discrepancy would be very noticeable, at least when playing chords.
If you were to use the same gauge string as your e string, and tune properly to pitch, that "B" string would be easier to fret and maybe, if there is a fretting issue, this would be resolved. I don't know. Maybe just ignoring that "12-gauge" string recommendation (requirement?) and going with a lighter set of strings might make things easier; a set of "11s" maybe.
Well, all these thoughts are pretty much based on my critical re-visiting my 1996 tonight....
I'd like to hear some other opinions. A few years ago there used to be a lot of 325 discussion here on all sorts of topics. I think a lot of guys went and bought bass guitars.
I had my 1996 out last night and was fooling around with the tuning. Man, I really like this guitar, and having spent so much time getting to play this well (11 years!)... well, I just couldn't bring myself to messing with the Mastery bridge and experimenting with off-intonation (sorry). But, at the first few plucks of the B string, I seemed to notice something different (I hadn't played this guitar in a while). I have my favorite couple of picks, and different picks do result in slightly different sounds. So, I played around with a few different picks. (I bought a couple of those Dunlop variety packs some time ago.) My favorite picks are thin and are flexible (nylon, Durlon). I tried a couple of relatively inflexible picks; Dunlop Jazz III and Dunlop Ultex (1.14 mm). With those thick picks, that snappy sounding profile of the thin picks flattens out. Just for the heck of it, maybe you can fool around with a few vastly different picks and see what you get.
Well, continued good luck to you. Your admirable perseverance reminds me of Thomas Edison's.
I tried putting some soft fabric material in the nut. This seemed to help, but just a temporary fix. What could I do as a permanent fix?