Read up on "Tramming" and it will get you going in the right direction... there are a lot of ways to do it.
If you don't have a DTI (Dial Test indicator... measures to .0001 inch or thereabouts, depending on model.) a somewhat less exact but dirt cheap method is to bend a piece of stout rod (1/4 steel round from Home Depot is good.) so it is kind of shaped like this:
If you spin that to one side of the table and get it to where you can just slip a piece of paper under it so it gently touches, then to the other side and you can get the same slip fit on the paper then everything is square. Otherwise you need to keep tweaking the column left/right until it's as close as you can get.
|______ <Bent Rod
That's probably why you get the ridges... it could be other things but you need that dead square.
LOL, kind of funny... you are a step ahead of me at the moment... I have been tweaking/improving/smoothing/cleaning mine for weeks... haven't actually used it yet, LOL.
The groaning sounds indicate the setup isn't rigid enough... something is shaking about. Check gibs, nut on back of column, etc or take lighter passes. How deep are you going, with what size end mill? How is the work clamped?