From your pics, I can see you have nothing connected to pin 4. That pin is what is directly wired to the on/off switch on the cruise control stalk, and pressing that button (momentarioy grounding pin 4) is what turns on the cruise light. Double check your stalk wiring with the diagrams, you've...
Sorry, I didn't keep good records when I did this job, so I don't have any specifics from when I did this on my vehicle, but all I did was follow the wiring diagram, the details of which I posted on the first page in this thread. That has the colour codes and pin numbers included for everything...
Oh damn! To go to your question of what could cause this, the bolts clearly fatigued. Only two reasons I can think why that would happen:
1. Lug nuts were over-torqued and caused the bolts to stretch, leading to poor/inconsistent clamping force along the threads, combined with the weakened...
Use a liquid gasket to seal it up. Arguably superior anyway. Downunder I'd grab a tube of this:
https://www.repco.com.au/car-care-panel/adhesives-sealants/gasket-cements/permatex-water-pump-thermostat-rtv-silicone-gasket-maker-14g-px22071/p/A9709957
Get whatever the US equivalent is from your...
If you don't intend to measure the LSPV pressures, your best bet is as you said try and mark the current position and match it. That did work reasonably well for my swap over. Obviously this assumes your current settings are right though, which may not be the case if you've done a big lift...
I'll make some time to work up a list. I spaced out the parts orders intermixed with other stuff over the year or so prior to doing the job, so I'll have to go back through the orders and separate and tally it all. The cost is concentrated in a few main key parts though.
Oh, this is probably overkill for what you're doing, but I did a full brake system rebuild thread here:
https://forum.ih8mud.com/threads/full-hzj80-brake-system-rebuild-booster-to-rotor.1316484/
Might be some helpful tips in there.
The small packets of red rubber grease you get in the rebuild kits aren't big enough, but you can order a tube separately. The rubber grease Toyota use is a Cosmo product, separate part number is 08887-01206.
Maybe post some pics? I did this fix, was straightforward enough with the youtube video as a guide. Either there's something you're doing wrong, or there's a physical difference with your setup.
Amber is the "rest of the world" spec. I think it's literally just the US and Canada that don't require amber turn signals. IMO it's a much better standard (can't mix up turn signals and brake/running lights), but you're in the US where anything goes, so do whatever you prefer I guess.
That's one of the most common aftermarket windscreen suppliers here in Australia too. I haven't heard of any issues with them. Pretty sure my current 80 has a windscreen from them fitted.
There is a small angle bracket that attaches to the module and the side of the accelerator pedal. I can't take an image easily right now, but I'll post one when I can.
Head gasket failures can give a variety of symptoms depending on exactly where the gasket has failed (ie, what's been connected that shouldn't be) and how significant the leak is. You have a head gasket failure. You don't need to see all the same symptoms other people have seen to confirm it.