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Check Fixture dropped and damaged - Cannot align to datums

Hey guys,

So I have a fixture here that was dropped by the operator before me, the fixture plate is quite warped now. (I had to shim one of the feet by 2.5mm) I did not clamp the fixture it is just sitting on 1,2,3 blocks. I took a bunch of points on it and constructed a plane and its giving me 2mm flatness deviation! Considering the tooling holes are no longer good I tried to use both a best fit alignment and an iterative alignment to try to Align to the datums but it doesn't seem to be doing the trick as I'm still getting high deviations on my net pads, also 4way and 2way also won't check good to .05mm. What would you do in this situation? Am I wasting my time?

Side note : I have a seperate program that is just a fixture alignment I used it, saved my alignment then recalled the alignment in my full layout program (After TB alignment). Everything is good to .05mm inside the fixture alignment program but when I recall it into the full layout the nets are +.3 and +.4 mm