After welding the frame, i did a quick check to see how straight and planer the two Y axis tubes are using a small surface plate with a DTI on a long arm. The surface plate was placed on a piece of plywood with three jack screws used to level the plate to three reference points on the tubes at the front left, rear left, and rear right.

Both tubes are now convex, and not planer. Measurements are below. Max deviation is 3mm!
I cant tell you how much is from the welding, and much was there before, but given that both are now convex my bet is its dominated by the welding.
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My original plan was to use shims under rails to bring them into alignment, but given the level of error I'm having second thoughts about that.
Is my only option epoxy?