Well, you aren't really helping diagnose the issue without fuel and spark maps. Tuning off hand controller or laptop? A 3D graph of RPM and load with AFR would really help to see if the car is tuned super rich or you have a fuel leak somewhere but you won't have this.
Flatspot at 2500rpm: Does it do it at any load/throttle? Is spark being pulled/advanced? Check AFR with a wideband? Where does the VVT switch(I have no idea if this is the cause)?
I would rather not do a TPS tune since you have a working MAP. Some ECUs allow two maps to be blended with different load inputs but I don't think micros do it; never looked into them too much.
Where are you? maybe someone could recommend a tuner who could re-tune it close to you specialising in microtechs.