In the interest of science and the curiosity of a one-time barista I did some informal testing this weekend. Very informal, very small sample size, mind you--I had no tastebuds other than my own for feedback.
Nearly all coffee shops use stainless for their brewed coffee. I've never heard complaints of strange metallic tastes; part of that could be attributed to some build-up of coffee oils. So I decided to brew coffee in several different materials. I wanted the material of the vessel to be the only variable, and so brewed all coffee by pouring 6 fluid ounces of boiling water over 1 tablespoon of (free trade organic) coffee grounds, my normal brew. After letting the grounds steep and settle, I decanted each brew into identical matching coffee cups.
In short, I brewed in titanium, stainless steel, aluminum, glass, and lexan. As much as I slurped, I couldn't detect a significant difference in taste between most of the materials. The lexan brew was ever so slightly... richer, sweeter almost? Sort of more oily?
I could develop this testing further if there's interest. Otherwise, just something to consider. From my findings, it seems like it's the mug itself contributing to the difference in flavor, quite possibly the shape? In reference to the temperature questions, I can say that my recipe for quick-rise yeast bread calls for putting hot tap water into a pyrex bowl--and plan on the pyrex bowl dropping the water temp about 20*F.