My bike does not hunt as bad as yours.
I have issues holding steady RPM between 2200 and 3200. It jutters but does not loose power and drop rpms like yours does for seconds.
Note I have a LAMS (learner) Restricted bike so this might have something to do with it - maybe.
I have the TB Vacuum hose mod - but I modified it to a looped hose system and a TAP, so I can turn on and off the mod - for me the mod does nothing discernible.
What really helped some things a bit was doing a TB synchronization. It has reduced it but it is still there.
Other thing to test is the O2 sensor, down low the ECU might not really measure the O2 but uses a fixed lean map ( I read that Yamaha XT660 singles are like this), but on the cross over point maybe like 4500 rpm the ECU kicks in and what you might be seeing is the ECU jumping between Real and stored fuel mappings - it is felt as surging.
see his products here that explains it - but nothing for us
another thing to look at is chain tension - it can exacerbate the feeling of surging.
I have also read that the sub-throttle sensor might cause it as well (advanced mod)
Try the simple things first. TB Sync and Chain tension and test O2 sensor.
Hoping it is an easy fix.