not a PC R (isn't that the "race" version?)
i have a part number 818-511 - 08 Touring
i thought the purpose of the PC3 was to be able to tune the bike and raise the RPM limit - without having the dealer put a 07 Sportster Stage 1 Flash in your 06 Road King (yeah, that worked very well)
Any dealer installing a Sportster flash shouldn't be working on bikes IMO. Not to mention an 08 has throttle buy wire and a Sportster doesn't, I don't believe they would be able to actually install that flash but who knows.
The PCIII does allow you to tune the bike and it allows you to raise the Rev limit to 6200 IIRC. No flash is needed. We don't do a lot of PCIII's but I think the PCIIIusb is capable of the rev extend. The model you listed has rev extend. It sounds like you need to enable it in the Map.