Every overdrive/distortion setting (even pre-amps) on my Boss ME-70 seems to be sounding REALLY middle scooped no matter what setting I dial in, to the point where its toneless and sounds really cheap.

I've recently adjusted the truss rod on my guitar meaning that the strings are very slightly closer to the pickups but amp ODs are sounding better than ever. Also I had to mess about with the input on my amp.

Any ideas on what could be happening?
Well, it COULD be possible that your strings being slightly closer to your pickups could give you a noticeable difference in sound. However, that would give you more high frequencies, not middle frequencies.

Then again, depending on your knowledge of how frequencies work and what does or does not make a tone sound "muddy," you very well could have been lacking high frequencies rather than mids, as you seem to think is the suspect.
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It's a Boss ME-70, the distortions are going to sound scooped, toneless and cheap. The real solution is to not rely on cheap distortion pedals for your source of sound and get a good amp instead.