I changed all 4 rotors, brakes and 3 of my calipers because the previous owner had spray painted them while on the car, the Rear drivers side went to complete rust and locked up completely and wouldn't move when trying to replace the brakes so I had to rip it off, rear passenger side was half locked up
so I couldn't get the brakes off of it either. The front passenger Bleed bolt was stripped so I just grabbed that caliper too while I was at it, was waiting a little before I replaced the final one, since I was getting some repair work to the quarter panel done and was a bit strapped for cash..

Since then I've had an issue with some grinding and squealing. Not at high speeds, about 30mph below its heard more. The Axle nut on the front passenger side became loose and I tightened it myself with a torque wrench and the squealing went away for a little bit (the grinding remained), but the nut became loose again and is once again squealing. The rotor seemed very loose when I took the wheel off to inspect it, and the rotor was grinding up against the brake indicator that had become a little warped and made a few gouges, but I also feel like there is very little clearance between the front of the rotor and the caliper and that's why the grinding noise persists, or is it just the brakes and the gauges. I can not determine if there is anything wrong with the front driver side, the rotor looks uniform in the brake pattern, so I am hopeful that it is fine. But over my engine and exhaust its hard to know exactly how the noises sound, I just know that they exist.

Struts, tie rod, the axle itself, etc. Besides the low caliper clearance idk what else it is, The backside looks and feels fine.

These are the gouges that were caused by the indicator/Caliper:



This is how far out the axle was prior to tightening it back up, currently it has protruded further out than this:



I am taking it all apart again in a few hours once the sun comes up and hoping that I can put the axle nut back on completely and it fixes the problem.
A video explained you can jiggle the wheel while holding at 12/6 to tell if your bearing is bad so I will be trying that also, I'm just not sure why the grinding noise is still happening.

Besides the wheel bearing going bad what other complications could be happening? Could the loose nut damage anything else besides the bearing?

Is my rotor ruined because of the indicator digging into it?

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The bearing thing sounds like a bad press job. Hope you don't need a new hub and or knuckle.

Did you inspect your caliper pins? They should be clean and lubed with non-petroleum grease. Dirty and or stuck pins can cause irregular pad wear.

Not sure if your rotor's toast. You can get it turned at a brake shop but Toyota says minimum thickness is 23.0 mm (0.906 in.)