I think one of the best places to start is to go to the Mikuni site and read the info in the Tuning Manual. Another thing is to forget how you tuned the stock carb, and don't compare the 2. The 42 has a much better separation of ckts and can be tuned individually where as I see there are more over lapping of ckts in the stock carb. I have run this carb without mods, with VOES mod , and TPS mod, I highly suggest the TPS mod and not even to bother with the VOES, there is enough difference to feel just by the seat of the pants, and does help with mpg's in city riding.

Some items to have on hand
#50 pump nozzle (leaner than standard #70)
and leave pump ckt at factory set-up
#98 needle (leaner than standard #97)
needle plays more of a roll in cruise mileage (65mph as per Mikuni manual)and is more geared for economy tuning, use the #97 if tuning for performance
Main jets same as stock carb (large head)160 is standard, have on hand 165, 167.5 and no need to drop floatbowl for only a main jet change, a 17mm nut is on bottom of bowl, main jet is right there.

Also might want to consider getting the short idle screw adjuster, I found that the standard idle adjuster gets a little tweaked since it will bend up against the push rod tube.
I'm using a mikuni choke cable since I was never 100% certain the choke was shutting off completely using the stock carb choke cable, however, the Mikuni choke cable is either on or off, there are no indents like on the stock carb cable


Yost Power Tube, if being used, be careful on seating it, it does not seat flat on it's collar, so don't try to force it, it is that way by design.
Be careful when removing needle, there is a brown washer that fits into a slight recess (e-clip on needle rests on this), it usually will not come up with needle removal, just need to ensure that it did not pop out of that recess. Do not use an extra washer for half-step adjustments either.

I will also suggest tuning by AFR. I am using the AFR table from this site: http://www.daytona-sensors.com/tech_tuning.html I have mine tuned to the leaner side (economy) of the AFR that they show for each ckt (use #98 needle) if you decide to use AFR on the richer side (performance) use the standard #97 needle