Narrowing it down to the preamp should help you a lot.
I don't think you need my advice. You've been doing just fine on your own.
But, I can't stop myself, so....
I would tend to trust that the model is accurate. I would definitely start with that assumption. I say that simply because of my previous experiences with questioning Cliff in some way or another and then finding out that he was right. I am just speaking for myself here. And purely as a matter of odds, I would expect the model to be very accurate.
And, there are these statements by Cliff/FractalAudio
https://forum.fractalaudio.com/threads/i-am-confused-about-the-jp2c.153540/#post-1826396
"I'm not at liberty to say anything more but JP himself gave the models his stamp of approval."
https://www.thegearpage.net/board/i...reviews-tones-questions.2124913/post-31011638
"Those are great amps. The particular amp used for the models was John Petrucci's personal recording amp. I didn't want to give it back and offered to buy it from him but he wouldn't sell it."
I know you are matching your particular amp -- which is a different situation.
So, I would look at the non-circuit items that could easily change, before anything else.
1) Obviously, and everyone has pointed it out, you have to set the tone and volume controls by ear.
They won't match the physical amp. You already know this.
You have probably already read about the "USA JP IIC+" model here:
https://wiki.fractalaudio.com/wiki/index.php?title=Amplifier_models_list
It is a must-read
-- also check the links and sources.
The amp guide entries have often helped my understanding on how to adjust an amp.
2) Tube brands can vary by a lot. Tube qualities can vary within the same brand. I don't know what tubes Mesa buys for their name brand. But, you might want to try out each of the 12AX7 tubes that are available in the FM3. See which one sounds the closest to your amp. The Mullard ECC83 is generally a smoother and less aggressive sounding preamp tube.
I couldn't find specific information about what preamp tubes JP might prefer.
But, Fractal's JP-IIC+ model uses a 12AX7A Sylvania, which may, or may not, be a clue.
And, there is this quote by John Petrucci:
https://www.mesaboogie.com/amplitudes/2016/June/John-Petrucci-and-the-Story-Behind-the-JP-2C.html
"I started doing some research about the different incarnations built in the 80’s. The various transformers, power variations, original Sylvania Tubes etc. and started to consider myself somewhat of a C+ connoisseur. I even knew to look on the rear panel for the hidden Mike B. inscription written in black marker that signified whether or not that particular MK IIC amp truly was a “+” version! I ended up gravitating towards a specific sounding version that I would bring on the road and into the studio."
My guess is that John uses NOS Sylvania 12AX7A's.
I seriously doubt that MESA is putting NOS tubes in their amps. Maybe -- maybe -- in the Limited Edition -- maybe.
-- Edit: I just checked. Even the Limited Edition uses the Mesa brand 12AX7'S.
3) Preamp tube hardness is a quality of the preamp tube. Once you have determined the preamp tube you prefer.
See if fine-tuning the tube hardness gets you closer.
I have dialed a tone in from memory -- and it was very close -- only to discover that some expressive quality was missing when I compared it to a recording. Dialing in a tone while the music is playing helps me to stay close to the sound I want. It may help for you to record the sound of your amp, especially expressive licks that make the tone stand out, and have the recording playing in the background while dialing in the model's sound. Your memory for details in a sound may be better than mine. But, this has helped me speed up the process.
This may not be important. But, the earliest JP-2C's had a different loop circuit -- only on serial numbers lower than JP-000345.
https://mesaboogie.zendesk.com/hc/en-us/articles/115003821813-Does-my-JP-2C-have-the-loop-update-
After you exhaust all the possible non-circuit variations -- preamp tube types, preamp tube hardness, and alternate control settings.
And if, you still want to try out changes that affect the preamp circuit itself.
I would leave the preamp tube bias adjustments as a very last resort
Preamp tube bias is determined by a permanent circuit resistor and is not adjustable in the physical amp
The Phase Inverter, PI, is part of the power amp. I would leave that alone and look at other things.
I hope this helps.
I will be curious as to how it finally works out for you.