12 bolt truck axles were ONLY used in trucks and only in leaf spring configuration from 1973-81 (previous years GMC's had them also).
If the spring perches are factory and they are spaced correctly on the axle, then I would start suspecting frame damage, worn spring bushing, bent shackles, or the flip kit is not centered.
NONE of these are going to be "perfect", but I would advise that you have room for tire deflections when trying to stuff the biggest tire possible for what you are finding.
Are the flip kit perches welded in and meet up to the saddles properly?