I'll just jump into what I've done and what I've heard. I'll say first though, that in metal, less is sometimes better. It's whatever though, whatever you like to hear! And that's said in encouragement. There's a billion different ways you can experiment, and I encourage experimenting, but here's the general rules I abide by:
I mostly always start with the the volume then wah first. The volume can be overpowered by dirty sounds or boosts. You can honestly put the tuner anywhere, but I have it right after the wah usually. Next, I would put compression, if you had it. Next, I'd do any dirt, in this order: fuzz, OD, distortion. You could put the noise suppressor right after, or in the effects loop of your Mesa to help clean up any "messiness" in your playing. After which I'd put modulation in the chain, octave then flanger. Then, your post effects like delay and reverb. Even try running the delay thru your effects loop, to bypass the preamp, to get a less "in your face" delay, unless you want that.
As for stacking tone, the Tubescreamer stacks very well with gain, and I would use it for leads, unless you're the only guitarist in your band, then I'd use it for a main sound. It might compress your sound some, but that might be okay sometimes, really depends on the day for me. I don't prefer stacking fuzz. It might do best just fuzz on the clean channel of the amp, but not mixing drive. Try it and see what happens (feedback might happen lol).
To sum it up, you have the perfect rig to be playing some Intronaut style metal! I'm liking the mix of vintage idea boxes with metal. Good luck in your tonal endeavors!
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