I had to replace my blue wire (alternator D+ I think) because the stupid P.O. broke it at some point and spliced on some half-assed thing that was just draped over the top of the engine shroud rather than bundled in with the rest of the wires like it should have been. IIRC it was 14 ga (I think the brown one is too) and I was able to find blue insulation wire only after scouring a few different places (including two Fry's - their selection was surprisingly not that good). Soldered on the correct harness end and "loop" end and pulled it through the bundle. Voila! Good, if not better than factory and I doubt any concours judge would ever be able to tell.
At the end of the day, it's just wire. As far as locating the brown color, try this site:
http://www.youdoitelectronics.com
They're located in Boston - I used to go in there as a kid. FANTASTIC place. They have everything imaginable for the DIY-er including "little stuff" like wire, fuses, project boxes, etc. A lot of amateur radio guys go there, which is a good endorsement. If they don't have it, I imagine they could get it. They were my next phone call before I found my blue wire locally.
EDIT:
Here's their "wire" listings - I'd call them about 14 gauge brown.
http://www.youdoitelectronics.com/id613.htm