OK, here I am, I've read everything, you've got a little hop or a bump in the steering. Front spindles turn fine, taking your rod loose from the steering box, you should be able to make the wheels move side-to-side freely.
Next thing, is there a bolt or a setscrew fastening down on the shaft? If so, make sure those are not hitting anything. You said you had the ujoint off, Correct? If so, other than the box being tight in the straight ahead position, do you feel any roughness or a metallic bump in the steering bax as you turn it from left to right? If you do, back off on the adjuster on the box slightly. Also, grab the input shaft and shake it. Any slack? Do the same where the steering arm connects. Any slack there?
If there wasn't anything in the box, its gotta be between the bob and the steering wheel. I read where you had some side-to-side play in the joint. Thats a no-no. Should have O slack, front,back,side-toside or anywhere else for that matter. Take the thing apart and carefully look at the cross and into the caps. Does it have any grease in it? Should have a little.
Grab a couple of rags, find a clean spot, lay those rags out. Get yourself something like a short glass jar full of solvent, plop those caps in there. Cleam all the grease out, wash the bearings and the cross.
Next, get a little wheel bearing grease on your finger, stick just a little into the caps, and put the bearings back in. Now, after all the bearings are in, get your ujoint tool or a vise, and squeeze the caps or slide the caps into the yokes and fasten them in with either the snaprings or the screws....depending on which kind you have. Usually its a press fit but I have seen the other kind too.
After your ujoint os back together, its tight and working smoothly....look at your steering shaft itself. On countless times I've seen folks rebuilding stuff because a steering shaft is bent and binding other component. If the steering shaft looks straight, connect up your redone steering joint, slide it onto the shaft and fasten it down. Has it got a thru bolt? A keyway, key and setscrew? Make sure these things are tight, and put a drop of loctite on the bolt or setscrew.
The steering shaft should slide right into the top of the yoke. Of it doesn't make it so that it can. LOCK IT DOWN! Now, if your piece of PVC that slide over the steeing shaft don't have alot of play in it, get a ubolt of appropiate side, clamp the piece of pvc to something. You want to hold that piece still while we perform a test.
With the wheel anchored at the top, thru a piece of PVC clamped to something anchored, turn the steering wheel, it should move smoothly, turning freely. Now, it its bumping in the same place repeatedly when you turn the wheel, in the same spot, like, evey 180 degrees apart, the ujoiny in 'camming'. That means you've reached the limit of angle that that ujoint can operate in and your gonna have to install another one, probably 6 or 8 inches above the last one by your steering box. (I had to do this on mine.)
Your steering shaft up at the top should have some sort of support or bearing. Usually what I do on the altereds is have a 2" piece of flatbar alum. bolted to the firewall, with 2 pieces if structural tubing (small, of course) or chrome moly, notched,bent and welded at the correct angle with bolt holes drilled in them. The alum acts as a stiffener in the fiberglass, the alum. in both inside and outside, sandwiching the fiberglass. Bolthoes going thru these, thru the tubing brackets. Across these brackets are a pillarblock bearing that holds the steering shaft firmly, precisely, in position.