Well, I'm irked that your shop was irked. Ordering a different length stem is hardly an unusual step to take to tweak bike fit and it's a pretty easy swap to make. Suggesting that you change your fore/aft position instead, when they know you have knee issues, is just all kinds of wrong. I have to wonder whether you're going to get the assistance you need from that shop.
At this stage, given your various issues, I think you'd be well advised to find a good fitter in your area. As a starting place to finding one, check out the websites for the bike shops in your area. I'd be willing to bet that at least one of them either employs a fitter or can refer you to one if they carry any custom bike brands, e.g., Serotta, Moots, Independent Fabrication.
Here's one that I found just doing a brief search:
http://www.trizilla.com/triathlon/pc/services.asp