Cool! Have fun.
No, bikes don't flood from running wide-open, they flood from having incorrect carburetor float heights (which controls how much fuel flows into the carbs. Or, the opposite: the float height is inhibiting fuel flow so your bike is starving for fuel--which is probably more likely. Is it possible that you're running it up to the rev limiter without realizing it? That's easy to do in the heat of the moment. Also, yes, make sure the engine is warmed up to at least 60 on the coolant temp gauge (no need for higher) but whether or not the engine was cold, that wouldn't cause the problem you're having. (Or am I wrong on this, YZF'ers?)
A few notes (of course):
I ran the Wednesday Night Drags (run-what-you-brung, elmination bracket racing (lose the heat? you're done for the night--it can make for a very short night...) on a full-on NHRA drag strip) at Sears Point (formerly knows as Infineon Raceway, now known as Sonoma Raceway) back around 2001. The first night, I took 2nd! So, I decided to keep going until I won The Big Plastic Trophy. Took a total of 6 tries and it was very satisfying because the night I won, there were 27 bikes (and yes, I did it on my '98 YZF).
And then I retired!
Seriously--after that first time, because I came so close, I *just* wanted that trophy and that was enough.
1) Burnouts help BUT you will drastically shorten tire life if you keep racing. Just something to be aware of.
2) If the back end breaks loose on launch (regardless of temp or burnout), it's not a lack of grip, it's releasing the clutch too fast and possibly combined with rolling on the throttle too soon. You're right--it's a delicate balance of launch RPM, clutch engagement and rolling on the throttle. But launching somewhere around 6-7,000 rpm, with a smooth, but quick clutch release (not popping it!) and faster throttle roll on is what you're looking for.
2a) If the front comes up a few inches, you've pretty much nailed it, just don't panic and back off. Peak power is around 11,500, so don't shift until then. I think (it's been a long time) that I got a faster E.T. *not* shifting into 5th at the end of the run, but I'm not sure about that. Just don't roll off the throttle until AFTER you've gone past the timing lights.
2a1) Clutchless upshifts are faster, so if you aren't good at this technique, practice it on the street so you'll be able to do it at the track.
2b) Also: KEEP YOUR LEFT FOOT ON THE PEG WHEN YOU LAUNCH because you'll need to catch 2nd gear pretty quickly. You aren't racing a pro-stock bike, you don't need to leave your feet hanging down, you don't have an air-shifter button on the bars, just basic riding technique.
3) Do NOT get "fancy" and use tie-down straps on the front end unless you purchase actual drag racing tie-down straps AND the fork-mounted brackets they attach to. No matter how tight you think you've made regular tie-downs, they'll come loose and that could be disastrous (like getting caught in the chain and tire somewhere in your run).
4) If you do want to get a *little* fancy, increase front tire pressure to max (40 psi? higher? I'm not sure what it is, just don't exceed it) for less rolling resistance, lower rear pressure to about 30-32 for more grip (larger footprint on the ground), and you can even lower the front end to make it less wheelie-prone (I once stood it up about 60-degrees off the line--not good for E.T.), but don't drop it more than 1" or you could cause interference with the radiator on a rough road/big bump (Very Bad). You could also drop the final gearing but then you're stuck with whatever you use when you're riding on the street (higher RPMs all the time, lower fuel mileage).
5) Always get and keep all of your timing slips so you can track your progress. There's a lot more to a good run than just the ET and terminal speed--launch time, 60' time, etc.
5a) WEAR EARPLUGS! Seriously.
6) At the starting line, don't look at your opponent. No, not an intimidation tactic, it's just that it totally doesn't matter what they are doing. And don't worry about their timing lights, just concentrate on your own.
7) Most of all: have fun.
Bonus note: don't race cars--those guys have no skill and might mow you down in their incompetence. (see: Mustangs and "Cars and Coffee" videos...)