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FWIW...I happen to own a White/ Blue 2005 Ford GT (no shit)...and it comes in from factory at 550 crank HP (very low rating - actually more like 620). It wasn't fast enough for me, so I changed the blower to a 4.5 liter Whipple running at 23 PSI to get to 1050 crank HP. Now it's fast, not as fast off the line as my AWD 991 TTS, but much faster at speeds!
Have you tried the Texas Mile with your Ford GT? 23#s is pretty good (no methanol I assume). I run 1.3 bar which I think is little under that, but with far less cubic inches ... for which there is just no substitute. Color me jealous!
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There are a myriad of "advanced" params - of which none are "magic". If they were, it's all you'd read about. Many are nuanced, many are not. Some dramatic changes can be made in some areas taken to extremes which can be seen in some of
@Danny Danzi videos.
The best method is to try them yourself by "sweeping" any given param from low to high/ full range and see what it does for you.
Beyond BMTBPD and MV and Input Drive, there are a few I do "go to" like Xformer Match and perhaps a controller (scene or CC/Pedal) on Input Trim. Some people, use things like Preamp hardness, crunch, harmonics, Low Res Freq., the GEQ, the preamp options, the power section (neg feedback, B+ time, variac, etc., the speaker tab options and the dynamics page options (dynamic pres, dynamic depth, character, compression, xformer match, xf drive etc.) Since you mentioned it earlier, Cliff wrote a section (tech notes) on power tubes and tone which might be of interest for you, but not sure what you are trying to achieve. We're just throwing darts at an unknown objective.
If "clean - Clean" is it - you can achieve that with gain reduction and a low gain amp, (Input trim at 0.5 and low Input drive) or keep your volume knob down on your guitar, etc. Some models are much more suited to this as you've already discovered. Lastly, most users have commented that with Q7.02 not much fiddling is really required as all the amps have been remeasured and new values adjusted by FAS to be as close to the amps they model.
Many things affect tone, compression, eq, gain, and responsiveness. Which are you going for? What is "missing" for you? An example would really help us help you. This has been asked many times and yet not answered - a sound clip or video link of a tune with a time stamp is often used to highlight a tone objective.