Burping air from system is key. Check under rad cap, before sun-up when coolest OAT of the day, after 8 hour engine cool down, while parked with front end higher than rear.
Properly installed: thermostat (OEM, w/ jiggle value at top), rad cap, and proper working reservoir hose and its cap are all a must.
All 3 radiator fins, need washing. Air passing through fins, is key to dissipation of heat. But typically, we'll notice ECT higher when moving slower or stopped. If fins clogged.
Keep in mind. The first rad is the A/T oil cooler. If A/T fluid (ATF) running hot, we transfer extra heat to condenser and then engine rad.
We are seeing some weak Aisin fan clutches. Some refill with thicker oil. Toyota Aisin FC, are build to higher standard. As such, less issue out if the box.
The 06-07 use a different fan and fan clutch (thicker clutch, w/black mount flange). You mention major engine work. Make sure the FC and fan, was not switched to older style (FC has blue mounting flange).
If we know all of coolant system, service properly (most I see are not). AT Fluid in proper range. Then we need to look deeper.
Good starting place, is watching fuel trims and AT temp.
What are ECT, fuel trims and AT fluid temps readings. While on HWY, off road??? If running lean, cylinder head temp goes up.
At higher RPM, fuel pump runs in high speed. It may be worth monitoring fuel pump speed, if you find fuel trims running lean at higher RPMs, as ECT temp hit your highs.
If coolant system serviced correctly and all as should be. Then we must consider work done! Blockage is what comes to mind. Not just in heads, but block must also be considered. We just had one in mud. Where a shop towel left in a port during service, was causing blockage. Blockage can just be slowing flow or total blockage stopping flow, in one or more passages. These can be very tricky to diagnose.
???? Why were the heads R&R? Replaced with used or new heads? Used restored, and possible boiled?
One of diagnoses best clues or starting points, is: Did issue begin, after a service.