When you say it started happening before the mods, did you already have the Akras fitted, and by mods do you mean the filters and PC? The reason I ask is your symptoms correspond to those of a blocked exhaust. Or blocked air intake for that matter, but I�d rule that out on the basis that you�ve just fitted new filters - unless you accidentally left something in the air-box of course!
The Yamaha dealer supplied Akras have cats and it is not unheard of for cats to break free in their chamber, rattle around, wear themselves into a ball shape and then eventually fall into the link pipe/collector. If this happens it can be intermittent, particularly to start with, as the broken cat sometimes sits in a position which lets gas through and at others blocks it, plus they move about as you throttle on/off. Eventually it may lodge permanently somewhere, or even get small enough to be blown out the tailpipe (if you�ve not got any baffles). The left hand cat could fall into the collector pipe and block both tailpipes, the right and one is more likely to just block the right hand pipe.
At tick-over and at small throttle openings a partially blocked exhaust system will flow enough gas to allow the bike to run, but not at high rpm. If you fit free flowing filters and get more air into the motor the symptoms of a blocked or partially blocked exhaust will get worse.
Did you notice any abnormal rattles from the exhaust system when this initially started happening? Might be worth taking the tail pipes off, give them a shake and see if they are clear. Check the rest of the system is clear also. If the baffles are in, their worth a look too, mine initially trapped a lot of fibreglass packing material that got blown out of the silencers.
Other than that, (as above) check the fuel system (fuel pump, fuel pressure, blockages, restrictions etc) and also the fuel tank breather pipe is clear and not nipped up or trapped. Also check the throttle body, intake hose and pipework for vacuum leaks, particularly if you took any of the hoses off or disturbed the intake when fitting the stage 3 kit. Have you got any engine trouble warning light giving any fault codes?
Hope you get it sorted.