I have three F.G., and commute on them nearly exclusively in the summer. I have built the wheels on all of them, one is a 27". Even building the wheels yourself (assuming you want a mid-level build), you COULD spend $100 per wheel for hub, spokes, and rim (figure $30 minimum for hub and rim each, then $1 per spoke, this is best case, and you will pay more for more better stuff). Like you, I spent the money as I liked the rest of the bikes. IMHO, the wheels are one of the most important parts of a F.G., so a lttle extra spent on better components is worth it.
Building wheels is not hard, but will take some time the first time you try it. If they get too out of whack during the build, then you can dissassemble it and start over. Besides some basic tools, you will also need a decent truing stand which can probably borrow.
You need to make a tough call, but there are more and more options on the 'new' market. The Redline 9-2-5 I crave, and this is what I would buy if I were to buy a new, non-track, F.g. (n+1 issue). Giant also makes a cool chrome F.G. whihc just went on sale here for $499.