I always found the 1000 was a bit soft until 3500 revs. A non working EXUP makes it feel worse although some do not think so.First port of call is check the EXUP is set correctly.Synchronise the carburettors set the idle and then set the TPS.
If it still feels soft then change the throttle tube to R6 type the models from 2006 onward, Easy cheap fix.
I always felt the 1000 had a very lazy throttle compared to other large capacity bikes I have ridden and the R6 tube sorted it, much more enjoyable to ride now