I can't see why anyone would want to open the ports up on the busa head, but then i don't build drag engines just circuit ones.
My opinion is the stock inlet port is far too big. Those with flow benches and pitot tubes will know why. The critical thing to be looking at on all these engines is port velocity and velocity profile through the port. Even on my 1580cc motors i reshape the port and run slightly less than stock intake port cc, on a 1397 or 1300 i am for much less than stock cc. But then like i said, my customers need repeated punch from as low as 4500rpm.
On 1000cc and especially 600cc motors, the small ports with correct velocity make huge mid and especially peak power gains. Different horses for different courses though i guess!
Oh and yes, bored throttle bodies cost power on 1400cc motors. Last time i tried it 1.5bhp gain for last 1000rpm but 3-4 loss everywhere else.