A quick update from this weekend, but without pictures.. was too busy and short on time.
The 4runner is still road-worthy it would seem. I got to the bottom of a couple of noises I was hearing.. Some sort of a new rattle was driving me nuts. I ended up pulling everything out of the drawer system, all the tools, literally everything.. come to find out, it was an upper link mounting bolt above the gas tank coming loose. I'm assuming from all the flexing and bouncing offroad. This is the really crappy one to get to so I'm guess I never get it quite as tight as the others. In hindsight I probably should just loctite the hell out of it and throw on a locking nylon nut..
I also found out that I knocked my rear diff skid around pretty hard and the front side of it was rubbing on the diff yoke. That resolved the noises I was hearing from the rear. Definitely have much more peace of mind now. I also saw that I managed to catch the lower shock mount on the passenger side on a rock pretty good. Feel pretty stupid for not re-installing my homemade skids for it.. At some point I will also have to address the lower link mounts as well since they're pretty banged up at this point.
Now onto the front.. I made some discoveries on my new steering setup that explain a lot of what I've been feeling with the steering getting tight in a spot or two. Checking for clearance in a static, hanging situation when building out the steering shaft was great. However, what I see now with the rig on the ground is that the shaft moved around ,A LOT. It definitely makes a bit of contact to the motor mount at some point in the rotation because I can see a scratch all the way around the circumference. Doesn't look terrible, and I'm more than likely going to just leave it until the next time I have the axle out since its the only way to get decent room to do any work up there.
The other point of impact I found was on the u-joint of the steering shaft. It also slightly impacts the motor mount/rail and has been the slight binding feeling I have been experiencing. What I did temporarily (until I build my second shaft) was loosen the connection and slide the u-joint back a bit to give me a little more room, which seemed to have fixed the issue, at least partially. My recommendation for other folks looking to tackle the LC200 is to experiment with positioning the rack back, not forward. If positioning it back isn't an option to the coils I would definitely recommend clearancing the mount and frame rail more than I did

it's proven to be quite a project for sure lol.
I think what I may do when building out the second shaft is use a flap disk to knock down some of the high spots on the u-joint body to aid with clearance and build out the splines 1/8" further out so it doesnt sit so close to the rack when mounted.
I also pin-pointed (at least roughly) the area of where some slight popping/clunking is coming from the steering shaft. Its on the u joint that is inside of the cabin right at the rubber puck. I can feel a slight wiggle there. Not sure if its coming from the u-joint itself, or something with the puck design.
I can tell you that when steering the wheel and watching the puck, even though everything is tight, I can see it lift up as it makes it turning motion. I'm guessing this is by design to help isolate vibration or something.. but can't be certain.. I'll need to do some more digging to see what this is. It's not bad on-road. But offroad when the wheels are going over medium speed rutted sections you can hear/feel it pretty bad. Last thing I need is to have something fail on the steering system
And lastly.. I'm back on the market looking for a decent brake setup.. my pad and rotor that took a trip off the car and into the woods aren't 100%.. the pads chipped up top as the wheel side loaded the rotor/caliper before it snapped and the rotor also has some surface scarring that I'm not sure is good to let live on the car long term. Considering getting some slotted/cross drilled rotors (though previously i have been super against these for off-road purposes) to help keep the heat down while they try to stop this whale during city/highway driving. This, along with the ABS sensors I just ordered brings my grand-total of the screw-up to somewhere around $1000. again, all in all, super fortunate that this is all that it cost all around.. not just financially.