I could not get my 07 XTX fuelling right with all my engine mods, even with a PCIII & many hours of tuning on the dyno with Tunelink software. The problem lies with the Yamaha software not the PCIII. That's why I back dated my wiring loom & ECU (pre O2 sensor), the PCIII now has full control over the fuelling.
I would wait a few months to see if Dyno Jet are able to come up with a O2 simulator.

There are many 07/08 riders waiting for a fix.