I'm Taking this incident as a "Glass half full" issue.

That's not good if the dealer had done that, they are both mounted with a 90 degree so they drop straight down the side of the battery

The key word, Mate, is "IF"
 
If one of the kind riders with a 2015 rocket X could take a look at theirs then we would know where the problem lies
 
The dealer picked up the bike today they ordered a new cable to replace the existing it is not as simple as just adding a new terminal end. Cutting only one half of an inch off of the battery cable resulted in it being too short to make the link to the battery. Hopefully I will get the bike back on Friday. The dealer has also agreed to reflash the ECU to accommodate the new exhaust I have installed. All will be no charge.