The problems that you are reporting sound very much due to the removal of the EXUP. When working the valve starts opening around 2000rpm and is fully open around 6000rpm which is the range where you say you are noticing issues. You essentially have an exhaust constantly in the post 6000rpm stage and are missing the benefits of the EXUP at the lower range which is to smooth out the power and increase torque. Your best way forward would be to get the system restored or find a complete racing exhaust which does away with the EXUP but these are getting very hard to find and are not cheap (do not get a cheap set of headers from SandySpares or similar).
Given the negative affects I can see no reason for a mechanic to remove the EXUP unless it needed repairs and this was not financially viable, i.e. why spend £200 when you can sell the bike on to an unsuspecting owner who then has to take the hit?
The main jet kit used is from Ivans Performanc Parts in the US it has nothing but positive impacts on the bikes performance.
Given the negative affects I can see no reason for a mechanic to remove the EXUP unless it needed repairs and this was not financially viable, i.e. why spend £200 when you can sell the bike on to an unsuspecting owner who then has to take the hit?
The main jet kit used is from Ivans Performanc Parts in the US it has nothing but positive impacts on the bikes performance.