It's been said many times, taking the exup out gets rid of the mid range, would appear yours is proof of that. A well set up gen 1 with ivans and an exup has plenty low/mid range grunt and not many have any complaints about it
If you want to get the best out of a gen2 with mods then its dyno time and a custom fuel map to suit your mods.
The EXUP valve is there to give you better low down/mid-range torque (closed) as well as top end power (open) so by removing it, you remove the lower end performance.
I would argue that if your only riding it in the rev range in which the mods aren't effective then would you not be better off with a smaller bike? If your only riding around the 3-6000 rev range then your not using any of a litre bikes potential regardless of mods.As you said you were searching for the torque of a twin, maybe look at an MT07? They are very cheap new so I'm sure you could sell a fully modded gen 2 fz1 for a similar price to a the cost of a used standard MT? Just a thought 😊