I think the next thing for me to figure out is what James Marchant meant when he said ...
He didn't build a JTM45 with a 12AU7 output stage. He built a 12AU7-output amp with a
JTM45 flavor.
He says, " an input stage ... then gain then anode follower then the tone stack ... Then there is another anode follower to the PI."
I think you should read that as "common-cathode gain stage" (the kind you already know about), Volume control (cause it's the only knob aside from the single Tone control), then common-cathode gain stage, the tone circuit, then common-cathode gain stage, then split-load phase inverter. We already know from previous discussion that he used the split-load inverter.
WTF is an "anode follower"? Well, in this case, he almost certainly means a gain stage with an output at the plate. There is a circuit in tube lore called an "anode follower" or see-saw circuit, but it has nothing to do with what is going on in this amp (and usually implies the use of 2 triodes).
"The 60s (JTM1) has an input stage that has a cathode r/rc network designed to imitate the frequency response of a jumpered input with a little more bright than normal volume level ...
This is easier than you think. The normal input (with the 330uF cap) is just insane mud. I know from having an early 70's 50w Marshall. The Brilliant channel is too ice-picky for normal use. Jumpered input allows you to use the volumes to get a balanced sound.
So I'd interpret his comment as having less bass than the 330uF cap, but more bass than the 0.68uF/2.7kΩ setup. Subjectively tilted a bit closer to brighter than darker.
I'd read the tone circuit as being a full-up Marshall tone circuit, but with fixed resistors in place of the Bass and Midrange pots. That way you control the overall sound with the single (Treble) Tone pot.
I think the next thing for me to figure out is what James Marchant meant when he said,
... There is about 6dB of NFB into the grid of the PI.
.
If you want an exact clone of the amp, you'll need some feedback from speaker output to split-load grid. 6dB worth.
... There are a number of interesting input networks documented in the books I have been reading. One of them might be fun to try... it has two inputs high gain and low gain. ...
If it were my amp, I'd just stick with the basic setup.
The folks I've known who had a JCM800 (the input setup that adds a gain stage to the High jack) never use the low gain setting. Of course, they also got the amp because it was master volume and they wanted distortion.