The best way to make a map from scratch is on the new Dynojet 250 or some dyno that has load control and exhaust gas analysis. You set the dyno to hold the engine at a specific RPM then twist the throttle to each desired opening (2-100%) then read the exhaust gas % and adjust the map accordingly at that throttle opening and rpm range. It takes about 3 hours to develop a map from nothing but when you are done it is right.
Assuming you dont have that its back to the old way of taking a map that is CLOSE then changing it. I have started with a map that is for the pipe and or airbox condition I have and go from there. As you can see on the dynojet supplied maps the airbox mod makes a huge difference in the required map. Even more so than the pipe brand.
The problem is even with a dynojet 150 dyno (which is really not a dyno but more of an accellerometer) you can only measure the 100% throttle. Since you dont have the ability to load (hold the bike to a specific RPM no matter how much hp the bike cranks out) you have no way to set the lower throttle positions from 2%-80% which are the ones that effect rideability most but effect the dynojet 150 reading the least since you always do the dyno runs at 100%.
In addition to fuel you can also change timing with the PCII from 1000-11000 rpms and every step in between.
All of the above described changes must be done with the laptop. Manually on the PCII box you can make crude adjustments that are roughly equal to those you can make with the yoshi box using the LED panels on the box. Low=0-3000 rpms, mid=3000-6000rpms, hi=6000 rpms and up.
I think your best bet is to go to one of the new Dynojet 250 tuning centers that are opening up across the country. I think there is a list of them on the dynojet webpage. Those people have all been trained by Mike Belcher at Dynojet and should be pretty good at it by now. If not you may be able to find someone