For big alterations, you can warm PLA up to 60C and move it around like plasticine. It’s a bit drastic though!
I would think that if it was a flexing issue it would be different in one direction of cut versus another?
Yes. I couldn’t tell from the picture whether all the ridges were in the same direction or alternating. That’s useful information and implies you’re on the right track looking at the tool mount.
If that tool mount is pla, keep a close eye on it while you’re using it for long runs. They cover most of the motor, so it’s not going to cool as well as the double band style mounts. When the router gets hot, it can soften the pla enough for it to loosen up.
If it’s still not straight after a new mount, might want to print a tall calibration cube in vase mode to make sure your Z is straight on your printer.
I reprinted the toolmount in PETG so that it wouldn’t be an issue. It should be vertical as the universal plate and the tool mount were printed on two different printers and they are aligned perfectly.
Try lowering your step over a little bit, I think that all actually looks pretty good. You have to remember with a 50+% step over some will be climb cut and some conventional so it will look different on each side. Smaller step over gives you a smaller angle error between passes and the same cutting direction. So it will be much more uniform.