Hi,
I'm not a seasoned 225 Honda tech. Just an old wrench that is more of an interested "armchair QB" these days. But, you asked for ideas so here's mine:
I don't know what you know so please excuse if I'm going over info or things you've already addressed.
After reading the operations descriptions in the manual, the two major performance components that "adjust" as the engine is running are the VTEC solenoid and the Inlet Air Bypass (IAB) solenoid.
The VTEC activates at 4500 rpm and above and shuts off below that speed. So, I have ruled that out for your hesitation since you say it occurs pretty reliably around 3500 rpm when newer and 3100 rpm as time went by until the recent timing belt replacement.
On the other hand, the IAB solenoid powers on at around 3750 rpm. So, that's close enough to make one wonder if there might be a correlation. But with your experience of the issue changing over the years and occuring at 3100, I have my doubts about the IAB being at fault. Also. I think if it were the IAB, it would likely cause a more notable loss of power over a wider rpm range.
You seem to have covered fuel delivery and, while it's not something I would readily rule out, I think it too would cause more of an issue over a wider rpm range than what you're seeing.
So, my #1 idea about what might cause a slight hesitation at a pretty specific rpm over and over again would be Throttle Position Sensor (TPS).
This sounds like a "bad spot" in the TPS potentiometer.
I would do a "sweep test" of the TPS using an ohmmeter to see if there is a resistance "glitch" as the the throttle is slowly opened and closed.
However, this test, using an ohmmeter, doesn't always yield good information.
A digital ohmmeter might not actually catch and display a fault well enough for you to see it happening. A high quality graphing meter would have an easier to read display but not always. (see below)
I have kept my old analog Micronta (Radio Shack) meter all these years because the sweep hand of the meter is very easy to follow when checking TPS.
But....
...because the event can happen so fast....(multimeters are slow)
....and might not even occur using the meter as the power source....
Most "good" auto shops keep an oscilloscope handy to check components like this "LIVE" while powered by the vehicle to obtain accurate results.
Besides the TPS, other things that come to mind for this would be an oxygen sensor or a MAP sensor.
Hope you find it.
Good luck.
.