We're headed down the same road with our '06 WR450FV's. I've had mine for seven weeks and I'm really happy I picked the WR! After spending all that $$$$ for the brand new bike I can't really blow thousands more just to have the fastest/coolest bike in camp. The titanium pipes, carbon fiber accessories and silly sticker kits aren't important to me. Out on the course, or trail, is where it matters. However, having owned and raced a YZ490, CR500, and 540DXC I have a good idea what I want from my WR450. For what it's worth this is where I started, and what I've done so far:
Bought and installed the AIS removal kit (GYT-5TJ93-69-00). Yamaha should GIVE this to ALL '05 and '06 WR buyers! It includes all the plugs you need plus a YZ throttle stop, an adjustible needle and clip, a 48 pilot jet, and detailed installation instructions. Right now this the BEST $40.00 you can spend on your WR. Also in the instructions are the airbox snorkel removal, gray wire disconnect, and exhaust restrictor mod. I bought the $60.00 Pro Moto Billet insert (05YWRINS) for the stock silencer, which they claim gives us 6.3 additional HP while staying under 96DB! I'm keeping the stock insert in my tool box in case an unfriendly BLM ranger fails me on the sound test, which can ruin a weekend. While at my Yamaha dealer I also got a few main jets (168, 170, 172), a 40 leak jet, and an MSR fuel mixture screw. I'm still tweaking (my jetting MY JETTING) the carb, but now I can go fast enough to determine what exactly I need to do with the suspension. Stiffer springs to start! INDY's now famous WR jetting guide (in this forum)is so accurate he could only help you more by installing the jets himself. When I'm done purchasing and installing my handlebars & hand guards, skid plate, big gas tank, and tall seat I'll enjoy years of serious screaming through the California desert!
Finally read this forum regularly! Many friendly, helpful riders post useful information here all the time. Info that saves us considerable time, money, and mistakes!