I charge by the sq. inch--ranging from 1.5 cents (simple edge to edge or panto)upward--I don't charge for thread (although know people that charge for each bobbin used on top of per sq. inch) but if I am having to use 2+ colors then I'm doing custom work, and the price per sq. inch is higher.
I don't charge for set-up---each quilt has to be loaded so don't think a set up charge makes sense. I do charge if there's prep work like pressing, squaring up backing (many people don't bother to do this), securing seams (just did a quilt that had tons of opened seams!), etc. Time is $$ for long armers, so having to get a quilt ready to load without charging anything causes a long armer to lose $ on the job. I don't trim bat/back unless asked to as many people want to do that themselves. I did hear Jamie Wallen say that he charges an additional fee/hour for micro quilting and haven't done that but it makes perfect sense--it's such a time & thread consumer!