I've had three motorcycles that I spent the money on to get dyno tuned ($425 each tune). Before sending the bikes off, I've always used the recommended power commander maps and uploaded them into the PC unit. Every single time, the PC map have given me an incredible tune and map. My custom tunes only accomplished around 2-6 gain in HP (06 gsxr750 3hp, 09 zx6r 2hp, 09 R1 6hp gain). The PC tune curve on the maps were always better then the custom tune. With that knowledge, I believe once you upload a PC5 map based on your mods, you will have a good tune. And if you're still not 100% satisfied, then add an autotuned which is still cheaper then a custom tune and will get you closer to an optimum tune. Now if the max HP is what you're looking for, then you need the custom tuning to accomplish that in a short period of time.
Another option people are gravitating to is to flash their ECU. The flash is just like adding a PC5 but they do the tuning inside your ECU. The good companies can give you an incredible flash that will have your bike running at optimum performance based on the mods you have on the bike. I've had some ECU's flashed based on the bikes mods and the end products have been incredible in throttle response and acceleration. These were friends bikes so I do not know how well the AFR is but at the seat of the pants they were always incredible improvements from stock. I've heard some people having horrible flash results but never from the first person perspective, just mostly hearsays.
