Are you still not seeing the CEL when you turn the ignition to on but not to start?
If not then you do have a issue causing that for sure, the CEL should be on until you start the engine and for it to be throwing the P0012 code the CEL should also be on when running, so I'm guessing the CEL is actually on but either the bulb is burned out or there a short causing it to not turn on, could be the wires you pinched and they may not be patched correctly or maybe when they got pinched it burned out the bulb or the circuit in the instrument cluster.

At this point since it seems to be running well I can't imagine the timing is off as much as the app is saying it is, I would try and track down why the CEL is not on, fixing that may solve your issues, or at least it will be one less issue you have, I know you said you tested the new cam sensor, but have you tried putting the old one back in to see if there's still an issue?

Ya, I'm still not seeing the CEL at startup, or when the code is thrown. In fact, I don't think I've seen the CEL on ever. The Center Diff Lock light barely illuminates when engaged, so there's probably some issues with the bulbs in the cluster I need to inspect.

I patched the 4(5 if including shielding wire, essentially 3 wires and 1 ground) wires that pass between the radiator mount and water pump. So, I think it one of those wires might not be completely patched and is throwing off the Camshaft Position Sensor.

I still haven't found a wiring diagram for a 2uzfe with VVT.

Here's pictures of the timing when I went in to fix the wires. This was as close as I could get the timing, the belt was lined up perfectly but when I installed the tensioner it slightly adjusted. So, these pics show the two cam shafts lined up perfectly but the crankshaft is just ever so slightly before the TDC "0" mark. Moving it spot on to the "0" mark, the cam marks were closest to the teeth that they are on, but were just slightly ahead kind of the vertical lines like the first pictures.

Also, there's pictures of the Torque Pro app showing the Advanced Timing and RPM, and after a bit of research the app is more reassuring than the dash tach which is ~500rpm's behind.

Sounds like you may be having some issues with your instrument cluster but your idle timing advance looks good. Service specifications state 10* BTDC (+- 2*) at idle.

Well, that's reassuring.

To be fair, I didn't get an OBD2 reader until after I did the timing belt change, so since there is no CEL, it could well be that it was throwing this code before I purchased it. (*shrug*, I totally didn't do an OBD2 read before buying)

I would just clear the code and then check for codes periodically to see if it comes back. If it does come back, then I would probably rule out the cam timing as it appears to be spot on and lean more towards an issue with your VVT system - particularly the VVT solenoids or clogged filters/screens. I think what's making the timing mark on the crank pulley appear to be slightly off is due to the angle the picture was taken.

You can easily test the solenoids by checking the resistance between the pins and also by applying 12v to the pins to make sure the solenoids are opening and closing. If the oil wasn't regularly changed, then sludge will build up on the screens which will affect the oil pressure to the solenoids which in turn affects your timing. My 2UZ-FE doesn't have the VVT so I'm not very familiar with this particular system but on the ones that I have worked on, the screens will be located on the solenoids itself or usually in an adjacent oil gallery in the head covered by a plug or bolt.

Thanks for your reply. I did clear the code and the code came back the very next day. It was a Pending Code after the drive to work(includes highway driving) and was a Logged Code after the drive home. I'm leaning towards the screen being clogged, I'm not sure the kid that owned it before me did much maintenance on it. Seemed like a project build that was sold to him and he just held onto it for a year or so. I'm planning on fixing a sag in the bag window this weekend, so I'll take a closer look at it then.

I checked the Oil-Controlled Valve on Bank 1(driver's side) for the code P0012 and although everything checked out with the multimeter, it wouldn't operate(slide) when hooked up to the battery. Ordered a new one off Amazon:

https://www.amazon.com/gp/product/B0...?ie=UTF8&psc=1

tested it right quick with the battery, operated perfectly and installed it. Haven't had a problem with the code since.

Now, I'm just waiting on those Premo Doug Thorley headers!!