Before you do anything, get into dealer mode to see the FI codes. The fact that it disappeared for a while could mean it's not O2 sensor related. Tell us the codes and we can help you, without them are all guessing.
I think it's worth emphasising that you shouldn't cut the wire, but rather remove the pin so you can put it back in if it's the wrong one. There's been a few threads on here in the past with people "disabling" the O2 sensor and then it doesn't work because the pin they removed was the wrong one (misinformation from Dynojet.)
The PAIR eliminator kit looks like it's the right thing. I removed the reed valves and pipes, but left the PAIR valve on the airbox in place. I simply bought some silicone plugs and plugged the places where the hoses connected to at the airbox valve and the cam covers. no need for an eliminator and it works a charm.
I wouldn't bother with a fuel additive, just put in a new oil an air filter, fresh oil, a new set of plugs to start with. Get a manometer somewhere, beg/borrow/steal, and balance the throttle bodies. Make sure the throttle position sensor (TPS) is set properly and while you're in there, wire the rubber throttle bodies boots so they can't come off by themselves (known issue.) All the info on how to do these are on the forum and there are plenty of people around that can help with advice as you go along. Take it easy and be methodical and you can't really get much wrong, these bikes are easy to work on. You'll learn a lot about your Vee and you'll save a lot in future servicing costs if you learn how to do it right now.
Valve clearance are a more advanced subject, might want to get someone that know what they are doing to show you how to do it as you go along. Clearances on the Vee are easier to do than on the Wee as the cams are gear driven rather than direct chain driven.
The rough running is fuel map related, the bike is leaned out around 4k RPM to pass emission regulations. A dyno session with a Yoshi box to tune the ECU is what's needed to sort it, BUT, as hookie says, you should sort out everything else first.