@silveradofab great update, thanks for sharing!
This basically confirms (in my mind) that the check-valve in the pump assembly isn't at fault (at least not in yours). For me, this also confirms that the high pressure switch is getting stuck on and not properly detecting when the pressure is high enough. This causes the pump to attempt to continue to pressurize, and I'm guessing because no more pressure can be built up, some type of cavitation is happening and causing the screeching sound, as well as causing bubbles to go back up into the reservoir.
I made a mark on my reservoir where the pump normally stops (when it stops). When I get the sound, I can visually see the brake fluid go below that line and the sound then starts. I don't get the sound before the fluid is below that line (ie, not enough pressure is built up, and the accumulator can still take a little more pressure)
cutting new holes for the 4runner version would probably work. One thing you might want to try is to hook everything up as best you can, electronics, and brake lines to the 4runner assembly in your 100. It might not "fit" enough to drive, but if everything is hooked up, you can turn the 100 on and see if it chokes due to a slightly different expectation when it comes to what is plugged into the electronics.
By retrofitting the 4runner part in, you're setting yourself up for some challenges down the road for future service should it be needed, because now your kind of troubleshooting a 100 and a 4runner. Also, what if the 4runner assembly is only tuned to deliver X amount of braking force, but the 100 needs X+Y amount of braking force.
I think the next step for me is to locate a donor pump assembly (or experiment on mine) taking it apart to look for the mysterious high pressure switch to see if a part number can be located. Hydraulic systems are not new and are not unique to the 100 series. I suspect these are "common" parts, if you know where to go and look.