You are building too high. Start with the swing arm level or a little less, and you will finalize your rear suspension as the weight comes on. Look through this build below, particularly page 4 where you will see how to change the leverage ratio to reduce wheel travel. It will be your final upper shock location that is the solution, but you cannot decide it at this time.
Set your front forks down to the build height you want for the frame/engine. As you add weight, you will start sliding the tubes back down through the triple tree to accept the load. I run my front ends with external stops, allowing the bike (with rider weight) to sit at the line touching the stops. At speed, under power, you will be off the stops due to aerodynamic vertical center of pressure. The bike will not settle onto the stops, on decel, until you are well below 100 mph. I can easily feel when my speed is low enough to sit up and turn out (and sitting up pulls it back off the stops). It only feels bumpy as I get close to the return road.
If you dont do this, you cannot bring streamlining close enough to the front fender for best effect.
CBR chassis build with shock location pic:
http://www.landracing.com/forum/index.php/topic,10559.0.htmlThis thread has a pic of how the front fairing is set up, to show why the carefully planned travel limit is worthwhile:
http://www.landracing.com/forum/index.php/topic,9761.0.htmlI have had good luck building without tires on the rims, bolting the wheels to my build table through the valve stem holes. Another helpful trick is to cut about a 6" section out of an old tire, to use as a "spacing check" during your build. You can tape it to a rim wherever you find yourself working out component positions. When its time to figure out your front fender mounting, you can put small wood blocks onto it, to be sure you dont violate the fender to tire requirements.
Building them is more fun than riding them!
JimL