When you print a pdf of the new part the holes aren't correct? If so in what way are they incorrect? The new part looks correct to me as a gerber in gerbv. The hole is .035 (which is I believe what you wanted) and the pad spacing seems to match the drawing above i.e. 5.011mm between the narrow pads 15.38mm between the wide pads and 29.3878 mm between the two pad sets taking the x y coords from the drill.txt file and converting from thou to millimeters. I haven't used the pdf conversion so I don't know how that works.
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