my guess based on the last picture is the left side loader frame is 1" too high, or right side is 1" too low.
if you can keep the bucket as is, loosen the left frame bolts, it might slide down a bit. If not enough, tighten them, then loosen the right side,then raise frame up a bit.
I don't know if there's slotted holes for adjustment , but there should be something.
I don't think the SSQA plate is wonky, as you can get box /bucket on-off ok ?
hmmm.... where the loader uprights 'slide in and lock'...... Are the tractor sections the same height off the ground ? Nothing in the WSM about 'installing loader frame onto tractor', probably cause it's factory installed...but if that piece was high, it'd raise everything high....
I don't know what's involved with the latches to remove the loader frame but maybe it's adjustable ?
I've never had mine off ( or the backhoe) so I'm looking at this from a mechanical point of view.
I do know mine's level, spent 4 hours bucket scraping 11 neighbour's driveways......