The power of disk brakes does indeed increase once the pads wear in after a few dozen stops. Disks are particularly sensitive to proper setup as well, and since there were a few other issues with setup of the bike (I still don't understand why you had to do it yourself if it was purchased from a shop and not online) I'd double check that if you still find the performance lacking in a few days.
With regards to the gear indicator, don't worry about it. Once you're familiar with the bike, you'll gain a sense of where you are in the gear range at any given time.