J,
I enjoy reading your blog. It's refreshing to see the reality of a build sometimes...the stuff that goes wrong, and how you work through it. Not comforting for you, but perhaps you can get some small shred of comfort knowing you might be helping somebody out there who has the same issues...
Anyway, I consider myself a bit of a maniacal do it yourselfer, and I abosolutely will go to all ends to solve a problem myself.
Here's my opinion on your issues:
You need a press to get those roller bearings down into the bell crank. I went without a press all my life until recently..I bought the hundred dollar 12 ton harbor freight unit. It's astonishing how handy these things are. With some scrap, some sockets, bearing driver kit, and this press, you are almost invincible. I agree with you, I would not try to punch or pound the soft-ish bearing shell into the bore. If you don't want to buy a press, go to a shop and throw a guy 10 bucks to press it in to the proper depth.
The horn wire tube. If it was me, and i didn't have a new-old ross box replacement handy, I'd see about making a new tube myself and brazing or welding it to the end cap. Do you have the original cap? Lots of folks say don't mess with the cap; once it's removed, there might be a problem trying to get it reinstalled and sealed. I just measured the tube on my box (it's apart right now) and the tube is 0.285' OD, and about a 0.031" wall thickness. I searched a bit and this is an odd size, and I could not find an equivalent. In this case, I'd search for a 0.25" OD tube and find a way to fix it to the end cap. Brazing would be cool, or perhaps I'd try threading the tube with a 40 or even 80 pitch die and double nut it (with thin jam nuts) onto the endcap. Seal with copper or brass washers and PTFE sealant. Not sure a nut would fit on the inside with that worm gear bearing close by...
Your disc brake flex lines do look to long, but I think you could perhaps come up with some sort of tether thingy that would keep it out of interference trouble. Of course you can only see what kind of interference hazards there are when the body is installed. But if it was me, I'd run it the way it is, as long as there's no apparent interference with other moving parts. Sometime when you get the time, get some shorter lines and install them then.
I think your pushrod is falling out because the body is not there to keep the pedal from overtravelling. When the tub is on, the floor pan prevents it from coming out too far. Maybe someone will chime in on how much "preload" the pushrod should have when the brakes are not engaged.
It's a bummer you don't have the tang for your clutch spring. I respectfully submit you should just accept that you might have some places where you're going to have to grind off the powdercoat and drill a hole, weld a tang, bracket, or whatever. As long as you prime and paint over the re-work, i think you'll never have a problem. Any paint, even rattle can paint, if properly applied, will far outlive the thin wash the Willys factory applied, and you won't even remember where your repairs are in a few years.
Your frame and parts look awesome, I hope you can get through these hassles. It looks great to me so far!