Steering shaft help.

Ok, so my '66 Mustang had a steering box with an integral shaft that can't be removed for installation. The normal procedure is to install the box through the column tube from the bottom...but due to my engine swap and custom longtubes its simply not possible to install the box that way with the longtubes installed....its also not possible to install the longtubes with the steering box already in place. What IS possible is to install the box from the top, but doing that meant making the shaft removable, so that is what I did:

I essentially cut the shaft, reshaped the box end to a standard double D shape and welded the Borgeson coupler on the shaft ide using rosette welds in the body of the coupler and a few corner welds at the shaft-to-coupler transition in an attempt to limit heat and head off any warping at the pass before it became an issue. Mission accomplished...no warping, the shaft is perfectly straight and now it unbolts from the box.

My issue is the set screws: As soon as I tighten them down on the double D side(either one, worse with both) It throws the steering shaft out of alignment...not much but by the time the misalignment travels down 36" of steering shaft the steering wheel side of the shaft is making a 3" circle. I would normally assume that it was my shaping of the double D end that caused the issue...but that isn't true since the smooth side set screw is causing the issue as well. I actually suspect the shaft necks down from 3/4" to just ender that right before entering the box(you can actually see evidence of this in the first picture where my sander line narrows as it goes back) In the end though I need a solution to fix the issue...it must be secured at the lower end but I can't have it throwing the shaft out of alignment doing so. I suppose one solution is to replace the coupler with an actual U-joint, but doing that would require me to add a lower shaft support in the column somehow, so any other suggestions are appreciated.

You don't need a shaft support with one u-joint--this is only a thing when you have two or more near one another.  This is assuming that you are still using the stock column for that spear of death . . .

The column supports the shaft.  I have thrown away a few of these things, so I can't remember if there is only a bearing at the top of the column, which could be a slight problem.  Steering systems can be so fun.  If this is the case, you can just get a bolt-on shaft support bearing/pillow block thing that you could bolt onto the inside of the firewall.  Check Speedway.

The other option is getting a rag joint coupler, which is what they did in 1968.

One more thing:  Unisteer makes a bearing that you can jam into the bottom of your factory column tube . . .

Yeah, what I have decided is just to replace the coupler with a U-joint after all, and add a bearing inside of the tube just to ensure the shaft has no way to wobble. I also chose a U-Joint with the set screws on opposing sides rather than at 90 degrees so I can better center it with adjustments. If that doesn't do the trick, then I will slightly build up the shaft where it necks down with weld and re-shape it on the rounded side. Between that I think I can get it without too much more issue.