Although it sounds like you work for or with a bike store and that might change the cost dynamic quite a bit, I generally caution against swapping things out on what amounts to an entry level bike. Ride the bike. Get some life out of it. Wheels do make a decent upgrade and you can always be used on a future bike (I like handbuilts myself FWIW), but hold off on swapping most other components unless and until they start to wear. Otherwise, you're putting money into a bike that might end up being your back-up bike in a few years anyway. From experience, a lot of cyclists end up itching for a higher end bike soon enough and any money spent upgrading their entry level bike, is virtually wasted. YMMV, obviously.

That said, I do agree that stock brake pads are often not so great. I used Kool Stop pads with pretty good success. A lot of people end up having to change out their saddles, too, for something more comfortable.