[alchemy]

39 and 40 axles, wishbones, and frames should all interchange in that area. And even if your spring was absolutely flat you should not have interference between the axle and the crossmember. Either you have some parts that aren’t what you think they are, or something has been modified.

Which brings me to the modification of the axle itself. Perfectly fine and common to drop the ends of an old Ford axle. Absolutely horrid idea to cut away the flange. Replace that axle, but also have someone who knows what they are looking at review the interference issue.

If the dropped axle is aftermarket, it may be narrower at the perches. This would require squeezing the wishbone together, thus pushing the axle forward. You should also notice the spring is now too far forward for a good fit in the crossmember, but maybe that slipped by you.