Rear end location wrong? IM STUMPED!!!

Your problem is the adjustment Equalizer in the carrier must be removed if you are using green bearings without adjusters or after putting one side in the other axle won't go in all the way.

Put one axle in without the nuts. Then install the other one you'll see It will push each other out.

The easy fix is to cut the axles so they don't bottom each other out. If you already tightened them you probably already damaged the retaining plates on the axles.

Measure the distance that the axles push each other. Split the difference and cut that much off each axle. Cut it 1/16 extra for clearance

On a Clutch style unit there are equalizer pins that can be removed they are connected with a roll pin. Cone style and open carriers the rear has to come apart.

Did you read the part in the OP's original post where he said the ONLY thing he changed was the leaf springs?

That would mean that the green bearings and disk brakes aren't new. Which would mean the green bearings aren't the issue with the axle housing not being centered. You sure as heck wouldn't be able to get the disks lined up in the calipers if the axles weren't fully installed.

If it were me I would ditch the green bearings and install the tapered bearings. Green bearings do not take side load. They are good for drag cars not for street. Your problems will be over.

There are literally millions and millions of Ford 9's on the street with bearings of the exact same style as the green bearings for the 8 3/4. They work fine on the street, and have for many decades.

I personally like having the tapered bearings, but saying the green bearings aren't good for street use is just silly.