You can only "infuse" something, such as peppers, into a liquid such as cream, water or oil with any reasonable success. You need to have a relatively high heat to pull the flavor from the peppers. Having made truffles a number of times, you infuse the flavors from items such as lime zest, lemon zest, peppers, or mint leaves by steeping them in heavy cream just below a simmer, then strain the solids out of the cream and mix that cream with chocolate to make the ganache.
In this instance, if you just want some chocolate to be tempered with a chili flavor, try using a dried chili powder or make your own chili powder and add it in small amounts to the melted chocolate as you are tempering it. DO NOT add any cool, water-like liquids to chocolate while tempering or it will sieze. Any water at all in chocolate will cause it to become grainy.
Tempering chocolate simply keeps the emulsion of the cocoa butter and the milk solids happy. If you've ever seen chocolate with a rather unattractive gray finish to it, that is called "budding" and means the chocolate was improperly tempered (or not at all), so as it cooled the emulsion was broken and the cocoa butter came to the surface. It doesn't affect the flavor, but it sure looks bad.
Hope that helps.
Moogs
Edit:No, I am not a professional chef, I just watch way too much food channel and am WAY too obsessed with the kitchen/cooking/candymaking etc. I spend more time in the kitchen than I do on ATOT...BLASPHEMY!