Are you saying the passenger side was low before you replaced the springs?
Did you say the tires stick out from the quarter panels? HMM.
The leaf springs have a bolt that holds the leafs together. The bolt head goes in a hole in the rear axle bracket. That positions it left/right, fore/aft.
It's possible the body is twisted. Maybe the passenger side quarter panel is welded on a little higher than the driver side. A unibody frame shop can set the car level at the frame
(your garage floor is very unusual if it's flat and level). Then measure to fender tops or where ever you want.
This may cost $100 or so but would be good info.
My '64 1/2 vert. Ordered May '64. D code 4 speed, handling package, caspian blue, accent group, Ford blue manual top.
'68 vert. driver. Owned since Apr '78. C code AT, AC, PS, P disc B, PT lime gold, standard black interior and top. NOS RF fender and left quarter.New top and folding glass.