Having the same engine I have had a similar issue before and here are some of the items I checked/did to correct the problem -
1st - Like BA said check/clean the O2 sensor -
O2 Sensor Info
Might want to check the "spark plug caps" I had 2 of the 6 spark plug caps that were reading open - they are resistor caps and should read 4-6kohms - If you have problems with one or more I would suggest replacing them all with the NGK Spark Plug resistor cover - PN LD05F - 8060
NGK
They work well and are a LOT cheaper than the yamaha OEM caps. This cured a low speed (idle - midrange) miss I had for a while.
You could also have thermostat problems - I had one that was stuck open. If you have not checked or replaced them it is an easy project and they are pretty inexpensive.
Make sure and get the thermostat gaskets if you replace them.
I have never fooled with my TPS but that might be worth looking into as well as the tiny fuel filter in the fuel injection pump.
You can go here -
Yamaha message board
do a search using OX66 etc. - there is a ton of good advise on that site.
Obviously there are lots of things that you can check and could be causing the problem - please keep us posted on what you find.
Good luck.