The fork stanchions on the 1946-48 forks are positioned closer together than on the 1949-onward forks. This requires a longer front spindle, amongst other changes. Without a set of early yokes to compare, I can't be certain what the difference in spacing is, but I think it is either 1/8" or possibly 1/4". In either fork arrangement, the hub is clamped by the spindle to the right side fork leg. My notes suggest a 1" offset from the brake drum for the edge of the (WM2) rim on 1946-48 forks but a 1 - 1/16" offset for the same rim for 1949 onwards. Is this the sort of discrepancy you have?
I suspected that this was the case but I thought I'd ask before tweaking spokes. The '49 yokes I have measure 1/4" wider than the '46 ones and the WM2x19 wheel from the earlier forks has a offset of 1" as you say. I will use this wheel with the later yokes and try 1-1/8" offset and see if it sits better in the forks.
I needed to replace the wheel spindle anyway - fortunately the new one appears to be the longer type.
P.S. Other work has overtaken the re-boring of my Square so it is running this year on the old pistons. If you still need them, they should be available sometime over the winter for you.
Same here - the '39 4G is sitting on my back burner so let me know when you get round to doing the rebore and I will arrange to come over to see you.