Not farting on the seat is ALWAYS a good idea!!!! keep the revs low(1/2 throttle or less) for the first 3/4 tank, then under 3/4 throttle for the rest of the tank. I did not vary my oil mixture. Honda seems to be doing better with the airbox seal but I would check the box/boot and boot/card junctures. I would check the spokes after each ride, they seem to loosen quickly. If you are in a moisture rich environment, (not NM) you should probably check the steering head and linkage for grease. The stock chain is junk, replace or adjust quickly, and if it's not an '04 toss the stock bars.
You can silicon it but the problem seems to be the metal ring that holds the rubber boot onto the airbox flexes and could allow dirt in, I think the 03's are better but I would reccomend a PC racing airbox kit or the MX
Bones ( I have heard good things about them but I haven't used one) also the PC kit comes with a little neoprene gasket that helps the filter seal with the aibox. I put the PC on form day one and have had no trouble, my buddy with the stock '03 was going through topends pretty quickly (he IS faster than me) but he resealed his airbox and isn't having as much trouble now. (lots of dust in NM)
you might want to give it one warm up and cool down cycle without actually riding the bike first, Ive read that is a good idea. Theres probably a ton of information if you search break in on this site.
SO, after work yesterday I rush over to my dealer, and low and behold there stood my brand new CR 250R ready and waiting, I tore home grabed my gear and went riding strait from there. I did about 5 km of open field riding varying my speeds, and then gently tore around the track for about 50 min or so, and then did some more open field riding. All in all, it was about 1 1/2 of time. So I am hoping after tonights ride of about the same, I should be able to really start walking on her, loving the turning ability of this bike it kicks ass.