I found and purchased a Akrapovic system. Can the dealer get the up map separately and load it onto my bike?
No... depending upon the year of the bike, it would either need the UPMAP key (after being reversed on the original bike) or, the later bikes used software and this would need a voucher creating after the original bike is reversed back to stock. Basically, the upmap is supplied only with the exhaust system and once installed, it needs reversing before it can be applied to another bike.
