I had a mate who "fightered" a CBR 600 and in doing so he removed the fairing which in turn caused all sorts of airflow problems to the air box. His bike would rev and run no problems at slower speeds but as the speed increased so did the flow of air being rammed into the airbox causing the problems you discribe (making the bike run very weak). This was solved by trial and error by decreasing the size of the air intake hole with about 5 pence worth of tape of all things (after he had paid out good money on 2 sets of carbs, numerous plugs & leads and various ignition components along with "
expert workshop time". £500 in total)
Moral of the above story -- don`t jump in and start spending money, unlike a true Scotsman
Have you altered the filter / airbox / carbs / exhaust in any way?
If there was an issue with 5th gear pitting or being damaged ,missing teeth, then there would be debris in the oil that you have just replaced, and if there was metal flying around in your gearbox then i am sure that it would have wrecked it by now.
From what you describe it sounds like a fuel / air issue so i would start there before tearing the engine to bits or buying things that are not required.
Kenny.