If it's just like the Ceria. layout.......the least I would do is raise the 820R to a 1.5K (2.2K for even more clean) and lower the bypass cap value to like 10uf
That combination might also get rid of some of the boominess in that channel 
I have tried. It is easier to change the cap. With a 12Ax7 I have actually tried many bypass configs. I am very familiar with what you speak, and agree in most cases. If not using the normal channel at all, I still have the problem. Last time I was in it, I found some plate resistors which had drifted. That boominess you speak of is the JTM 45 tone. It is present in the original. Not as boomy as it seems on paper. Back then we used treble boosters or if you wish a dallas rangemaster.
Thing is a JTM 45 with El34's does not have the wattage, so it suffers using a 100 watt cabinet. There is something going on with the tonestack, but I also wanted voltages from TG's build. I am simply going to change it to a 50 watter as I think the JTM 45 stock is about 36 watts or so. Since I have put a plugin ss rectifier, I may increase the filter cap values. The tonestack will begin overdrive about 12 oclock with any pot. I do not like the Presence sweep either.
I am looking to get a clean from buckers. My idea of clean may vary a little from yours. It is easy to get
overdrive from an amp, but getting Two Rock clean is a different story. I did not write nice overdrive.
The amp is loud compared to little amps, but not near as loud as a JCM 800. When I wrote it wasn't loud, I was comparing it to other Marshalls, not a Deluxe. I built this amp while doing other projects and have not spent much time tweaking. That being said, I have an original and an original plexi. The direction I am going with it is I have a new Heybour OT, 50 watt (copy of the Drake winding) I am going to install as I think the OT from Mojo is saturating, well I know it is. I will get it, no problem. I just wanted a voltage basis to refer to since mine have changed and also find out what others have done. I also plan to use some relays to make Doug's hotswitch and a couple of other tricks to make it 2 channel.
IMO, a 5751 sounds best in a Bassman in v1 and it is fine in this JTM 45, but a JTM 45 never had EL34, the distortion is coming from the preamp. I want it to be HiFi sounding and then hit a footswitch and get nasty.
I have friend that lives at the Metro forum who has done this, but he had lots of help and really is just learning so he doesn't know what he did. Someone else helped him and he did not record the changes. I played the amp, but I did not open it up. Anyway, I will get it. I was just curious how TG's turned out.
It is really a crazy idea to want a clean Marshall, but I have a 100 watt superlead which has the most beautiful clean tone. SG, thanks for your input. All comments help and get me thinking.