If its overheating at speed, when airflow through the fins should be maximized, and the fan clutch would be disengaged, etc (not needed at high speed...)...but NOT at slower speeds, the problem is unlikely to be related to the fan.
If the coolant passages are clogged, they would allow sufficient flow at low engine speeds, and become critical orifices at high flow rates when engine rpm was higher.
This would mean that at high engine rpm, the engine could not shed enough heat...and would get hotter....but, when the rpm was low enough, enough coolant would flow to carry off the heat.
That would be my first guess as to a possible explanation.
After that, I'd consider frictional issues, as higher rpm generates more heat due to friction, etc. Perhaps this is where the head work came into play...except that didn't fix anything.
So - As a Plan A, consider coolant pathways, and possible constrictions.
An easy fix is a hose that collapses under suction, after that, clogged coolant journals, etc.
TJ's Build Thread
2001 Xterra SE, 2003 V6, 5 spd, Shrock Sliders, Bumpers and Skids, Warn 9.5xp Winch w/125' MasterPull II, OBA w/4Gal Tank & 4 CFM Compressor, Revolver Shackles, Deaver 3-Pack + Calmini 2-Pack + OEM Leaves, Bilstein 5150, SLR UCA, Diff Drop, 3" SL, 2" BL, 33x13.5/16 LTB's, Snorkel, Electric Fan Swap, etc...