Okay, so I am going to dump a few measurements I took with a feeler gauge here... Because I can't take the guitar to a pro right now, everything in Quebec is locked down (Gotta love covid).
The action at the 12th string is .100" (low E) and .096" (high E) with strings unfretted, so the action seems to be in reasonable ranges.
The scale of the guitar is 24 3/4". From nut to 12th fret (low E) is 12 3/8, minus about .015" and (high E) 12 7/16 minus about 0.025". Nut to saddle (compensated) is (low E) 24 31/32" and (high E) 24 3/4. I don't know what this says about my guitar.
Neck relief : Capo 1st fret, string held down between 12th and 13th fret, at 3rd string .009" at 6th fret. Maybe a little low? If I add a little bit of relief to bring it up to .010" or .011" as I see recommended on some websites, how much action height gain will this incur?
Nut height : (low E) .004" and (high E) .005" with capo between 4th and 5th fret. Maybe a little bit low, considering one website I was referring myself to for the measurements says he starts at .008" up to .013". However, I don't have any string buzz, so I don't know what this affects.
From what I can gather with the reading I've been doing while taking my measurements, it's down to either a badly setup compensated bridge or an improperly placed nut.
I added photos of my frets from the first two frets, they don't seem too too bad. What do you think? And, also a photo of the relief of the neck.
https://app.photobucket.com/u/swordf...0-5836772f16b9
https://app.photobucket.com/u/swordf...b-893f6d5acb3c
https://app.photobucket.com/u/swordf...9-4b237de7746d
https://app.photobucket.com/u/swordf...e-cd320af4bb18
EDIT:
Okay, so it's when you read and read and try things that you learn. I had swapped over to light strings a few years ago (was sure I was playing MLs, but I found a new set of lights in my stuff and I always buy a few packs at a time), so I tossed on a new set of mediums (that the guitar originally came with) and all my tone issues are gone. The sound is a little more mellow, less crisp I find, but the tonality is right back to where it should be. Lesson learned. Thanks for all your advice and input!