I've discovered something interesting and annoying. It turns out that my right handbrake cable has totally seized somewhere within the outer sheath, in a partially engaged position, and was causing the handbrake to drag on my right wheel. The interesting thing is...I think it was like that during my E85 tune!
I spent a few hours under the car on the weekend to figure this out. With the handbrake off, I could see that the lever on the left caliper was fine, but the lever on the right caliper was noticeably in a semi-engaged position and difficult to move. I removed the right handbrake cable from the car so I can replace it, and when I disconnected it from the caliper the lever immediately disengaged the rest of the way (ie. the lever and spring on the caliper is fine).
I've already ordered a new cable from Toyota, and I ordered the left one too. I figured I may as well replace both.
I don't know how much a dragging handbrake would influence power on the dyno, but I do wonder if this explains why we initially needed to add a surprising amount of ignition timing just to make the same power on E85 as on 98 fuel. That had been puzzling me because I've heard that E85 is supposed to make the same power as 98 fuel with the same ignition advance (I don't know for sure if that's true though).
I guess I now have even more of a reason to go back to the dyno yet again! As I said earlier, I think I also want to add more timing at low RPM as I should have done in the first place.