The starting problem suggests something is out of spec so your first step is to have your dealer use a Mathesis to check TPS and other sensors, sync the butterflys, set CO, airbleeds etc.
I'd also have the cams degreed.
I'm assuming also you're running Pipercross or oiled stock air runner filters to avoid stealing volume from that huge airbox, on of the reasons for which is filling-in that mid-range hole..
The dip at 4-5,000 is characteristic of the 748R. Experienced tuners have had only limited success in minimizing it. A Power Commander and seat-of-the-pants dyno work won't give you a better result.
So yes, lots of people have been down this road. Here's a good place to start.
http://moto-one.com.au/performance/748r45ex.html http://moto-one.com.au/performance/748r.html http://moto-one.com.au/performance/748rnoport.html