I'd snip C9 right out.
It boosts above 333Hz, which is not what -you- want.
Using no-cap here reduces gain and small distortion, which is where you were going with the 12AY7.
C21 looks dubious for your taste.
For a more-classic "clean" amp, I'd bypass the whole V1B stage. This is adopted from Marshall's high-gain plans, and may be too much for some.
> The tone stack on this amp is the most UN-responsive I've seen.
The 0.001u cap on the end of the tone-stack is just "wrong". It loads the thing down (perhaps why they had to boost-back the highs with the other mods). It "might be right" if you work V2B to the MAX, then C13 takes some of the harsh off the sound. But if you are not flogging V2B past heavy clipping, C13 just makes the tone-stack not do much.
> tweaked to sound good overdriven.
Perhaps spot-on.
If you really want clean, no ear-bleed scream, then you might snip C8. Gain goes down and V1A's non-clipping distortion goes from 5% to 2%. However the huge values suggests they may have a hum problem, somewhat controlled by super-bypassing V1A cathode.
Is R25 really 68K? A more traditional value is 82K. It "should be" equal to R24, minus the loss through V3A V3B cathode coupling, times various other parameters. A slightly low value leads to slightly increased even-order distortion (below clipping) in V4 V5. That may be the intent, it may be fine; but you might try tacking 470K across R24 (to make that 100K lower in about the "right" proportion). I don't expect any "Wow!" difference.