I find the cause of my problem...finally!

Ended up costing more than another low mile engine, the prices of the engines went down, and prices of machining went up due to the pandemic during the time I rebuilt it.

Cylinders were honed very slightly, but these blocks have a factory coating on the sleeves, so you cannot bore them out, they don't even sell oversized rings for these. There's a spec on max wear on bore, this engine was quite a ways from that.

New parts:
Every single gasket/seal/o-ring/etc was replaced. Some I dealer ordered because the includes ones were not the same material.
All the timing components were replaced. Chain, gear, hydraulic tensioner, expensive dampener on the one camshaft, etc.
New VVT solenoid, oil pressure sensor, temp sensors, all electrical parts that went on the engine were replaced including a reman throttle body.
New name brand water pump.
New Toyota OEM piston rings.
New spark plugs.
New main and rod bearings.
New motor mounts as the old ones were pretty ate up.
Head was fully cleaned, new seals installed, then leak tested.

I had $1,600 in it. That was doing all the assembly myself and a shop doing the cleaning and machining. Parts alone were around $900.

The most labor intensive part was putting all the lifter cups in, because you only have a few thousandths of tolerance on each one, so you have to kind of play whack-a-mole a bit.

Here's a shot of the engine during assembly.


Now you can get engines pulled from low-mileage wrecks in Japan for around $1150 to your door.