you say you ran the stock setup for 3 years without trouble?
Seems strange that this happened all of a sudden.
I hate to sound stupid but are you 100% that the gauge is correct?
Is it puking water out of the overflow?
.....the original Tstat had a small hole in it to bypass water by the stat, Hondas use a bleeder screw below the water neck. If theres no water on the stat it will not open.
You know more about what has and hasn't been done, I'm just grasping at straws here to try and give some ideas!
Also... I dont know how your mechanic flushes the system out......but I always take the upper hose of the rad, start it up and let it warm up, all the while keeping the radiator full. (thru the upper hose inlet)
when the engine temp hits the Tstats temp water will start POURING out of the upper hose. I then let it run till it the water coming out of the upper hose is clear.....
This lets you know that the entire system is clean, plus because the water must go thru the rad, engine and the Tstat.....you know if its flowing adequately.