Buy the right bike in the first place! Nothing wrong with that Jamis, but at the end of the day, it's just a fairly basic hybrid, Going custom is really for high end bikes, if you are looking at the lower end of the market, just chose a bike which has everything you want on to start with, there are plenty of options out there.
For the options you have suggested, 1 = expensive, and 2 not may bike manufactures sell frame only unless very high end, or end of year closeout