I'm sure your motor builder friend and others will confirm that all the components of the motor need to work together to produce the max horsepower, but on an EFI setup the mapping is the biggest varaible simply because there aren't alot of guys who know how to do it properly. The shop needs an inertial dyno so that they can measure air/fuel, under load, at useable throttle positions and rpm. That's where the big dip in torque comes from in the dyno sheets that you refer to, not necessarily because a guy is using a two into one or duals, believe me, I have no such dip in my sheet.
As far as parts go, you'd have to talk to Brad Yuill about that. He did the headwork and the cams are ground for Freedom by Andrews to their specs. Understanably, Brad won't divulge the details. I can tell you that the pistons are stock. I have a gear drive setup.
You mentioned reliability. I ride with a group of folks (about 40 of them) all of whom have Freedom work on their bikes exclusively. Each of them has had motor mods ranging from air cleaner, pipes and Power Commander to superchaged 116's with head mod's, cams etc. Not a single one of these bikes is built to exceed 6200 rpm (stage 1) and the vast majority are built to the 5700 stock rev limit. The power comes at passing rpm usually somewhere around 2400-2800 and extends as far and as strong as it can with the components employed. The reliability comes from the low rev limits. A lot of these dyno sheets are similar in terms of peak numbers. I haven't seen any which can achieve more torque at lower rpm's with as wide an rpm range as these guys. Seems to me That's what you're looking for.