Late to the party, but might as well throw in my two cent worth. I see the
Kitchen sink has already been thrown. Looks like lash to me. The problem areas being 180 degrees apart is usually a tell-tale sign of lash. The reason why most of the ridges are gone when doing a very small step-over, or fine finish cut, is because there is most likely not enough force to shift the machine from one side of the lash to the other.
Also, I would definitely brace the gantry, as stated before. It's a simple procedure, CHEAP, and if it don't help it, it certainly won't hurt it. Regarding the indicator and flex, that should give you a good "before and after" measurement. You will never get all the flex out of it though. I can put an 0.001 indicator in a bridgeport spindle and get lots of needle movement with not much hand pressure at all on the spindle, or the table, or any other moving part. Everything needs clearance to move.