@bunny: First of all, I have not congratulated you for getting the Blade

Congratulations, it is a stunning bike, and easily the class-leader.
Thanks for those pics from the service. It is giving all of us a fair idea of how Honda is going about with their CBU program, and along with Fireblah's initial reports, is giving invaluable feedback to prospective and current owners. Keep up the good work.
As one of Yamaha's earliest customers, I also went through similar experiences of people not knowing what is where etc, but that was only in the initial one month or so. I'm sure even Honda will get their technicians up to the mark soon.
But the glue on the plastic clamp is unforgiveable. It smacks of our usual habit to cut corners and "adjust". That I can safely assure you is not present with Yamaha. For example, in the process of working on my R1, I have damaged a bolt, fasteners etc, and each time, they would adamantly change it with a new one. Yamaha's service did screw me a couple of times, but not in this way. This is pretty bad.
I don't know if it's the battery per se. This is elementary, but did they check the charging current? (Both while at idle and while revving)
Also, do you have warranty on your battery? Reason I ask is, the batteries on Yamaha's CBUs do not come with Yamaha warranty, but manufacturer warranty which is pretty useless since they do not have a presence here