What raska says is pertinent, but only if you have this problem when NOT in reverse.
In your case, although the 'poor running' may seem to have just started, it likely has done it all along. The Rappy has a reverse RPM limiter which is turned on when you put the bike in reverse. This limits RPM in reverse to limit your backwards speed to what Yamaha deemed a 'safe' value.
Unless your reverse switch was somehow stuck in the closed (not in reverse) position, and suddenly became unstuck, you should have always seen the limiter kick in the moment you shifted into reverse. An indicator that the switch had been stuck would be non operation of the reverse light with a return to operation now.
If you wish to eliminate the reverse limiter, simply connect the green/white-stripe wire, which leads from the reverse switch to the CDI, to a good, clean ground on the frame or engine. The CDI will now be fooled into never seeing when you put the bike in reverse. Your reverse light will not work as a result, but perhaps, a small price to pay for being able to have viable power when backing up?
'01 Scrambler 400, K&N
'02 400ex, piped, jetted, K&N, Lonestar +2 A-arms, Lonestar anti-vibe
'02 400ex, DiamondJ +3 A-arm widener, Lonestar anti-vibe
'02 660 Raptor, DiamondJ +2 A-Arm widener, YFZ shocks, LSR anti-vibe, piped, jetted, K&N