Have just finished machining this and as you can see in the picture there are still lines if I machine this way, it was machined from bottom to top at an angle of 315 degrees using a brand new 1/8 inch taper ball nose cutter that I bought from USA (Think and Tinker) I am now going to go and check the meshing as you have suggested (Gerry) the lines at the bottom of part are not very visible on picture as the wood there is lighter that the other side.
Thanks
Alan

I love my two sets of Festo clamps

Yes very good but not so cheap to buy here in the UK.

Somewhere over $100 here for a set, no discounts either. I bought mine a couple of years ago, first set came with the folding work bench. I have several Festo tools LOVE them all. Their straight track guided circular saws are awesome. What a great system to cut large panels out of larger sheets. Adjustable speed, straight, clean cuts every time.

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.