I've rebuilt my Nova suspension with stock parts.
Now it sit 2-3 inches high on one side.

1st - I'm questioning whether the upper control arm bushings and struts were pressed in properly.

Is there an alignment procedure to ensure the struts are at exactly the same angle on both sides before pressing the bushings in?
These front suspensions are coilspring over shock w/ upper and lower control arms. I am confused by your use of the term "strut"...
There is no orientation required for bushing install.

Right now, one side (upper control arm) looks higher than the other.
Did you torque the upper cross shaft nuts and lower bushing bolts before setting the car on the ground? This will "lock" the bushings and may cause height differences like you are having.

2nd - all rear leaf bushings and shackes are loosened, or is bushing alignment before tightening part of the leveling procedure?
Bushing alignment is not an issue

I believe I have miss matched spring rate rear leafs.
Are the springs brand new? If not, one or more leafs in the pack could be broken unless they are mono's...

When I jack up the low rear side with lossened eye bolts, everything gets a lot better.
That makes since...