Silverone,
I woudlnt worry about the shim, fwiw ( baisley and zippers both make them i am sure someone else does as well), because you have a high flow pump already in the bike. I would swap out my bearings, consider a good set of lifters, although you may have them if you have the 07 bike in that you would have the 99b lifters which are fine to use. If you go with the kuryakyn cams you might consider a tapered pushrod so you can eliminate the rubbing at the top of the pushrod tubes. The builder might also consider going slightly tigher on the turns .. eg SE recommends 2 1/2 turns or 15 flats but you may want to go 18 flats or 3 turns. I would consider going to the S&S 58mm throttlebody over the ones available. not sure what pipes you are going to run, but a good 2 - 1 with falsie or a 2-1-2 like the complete unit from Kury should compliment the build nicely.
who is tuning this for you? and what tuner are they using?
Good luck,