Mark,
I was debating whether to buy the parts and have my dealer install or send the whole motor to Zipper's. So I decided to take the 3.5 hr drive north to visit them and check out their operation. I met with John K and he was very accommodating, he walked me through his entire operation. I was impressed by the attention to detail and knowledge of the staff, these guys are really into motors and what makes them go with an emphasis on reliability, that is their specialty. I am pretty picky and ask a lot of questions and John answered them all to my satisfaction. I was convinced at that point to let them do the build.
One thing everyone needs to understand, they are a fairly small operation in that they specialize in parts and performance "kits". They have limited space and staff to do a "turnkey" job (i.e. drop your bike off and have them do all the work). They will do it, but it will take time. Similarly, if you drop off your motor (which is what I did) and have them do the build, they basically have one guy who builds the motors, so that takes time too. But in my case it is worth the extra wait. When they are finished, the engine has been heat cycled, ready to install and ride (with appropriate break in procedure of course).
I am doing the whole enchilada, diamond cut heads, cylinders, thermo-coat combustion chamber and piston top and skirt for heat management (may want to consider this option, not expensive), also sent my headers to Jet-Hot to have them coated after Zipper's welded in the O2 bungs. Also having them back cut my trans. gears and went with their double roller bearing billet trap door to beef up my 5 speed. Ordered a Rivera Pro clutch to put it all on the pavement and of course the Thundermax ECM with AT. I'm getting excited just talking about it!!!
Letting Zipper's do the work is the best way to go. JMHO.