There are many wonderful protocols out there to clean slips for cell culture, I have used several, some which include acid stripping, sonicating, and autoclaving. You are right about residual ethanoll, the tiniest amount will be toxic to your cells (no liver :-). A method I settled on that allows for bulk preparation is: 1) put a standard pack of slips into a 500 ml beaker, 2) wash 2-3 times with excess 70% ethanol, 3) rinse 2 times with 95 or 100% ethanol (this removes water and helps reduce the slips sticking to one another), 4) place foil over beaker and autoclave. This way you can prep 100 slips at once. As long as you open the beaker only in the laminar flow hood, you can use the entire set of slips without incident. Some people simply store slips in 70% ethanol and then take them out with forceps and flame them, the put them into the dish. If you flame too long the slip with splinter into pieces and this is time consuming.
One question I have though, are you placing a glass slip into a plastic dish (with cells on the slip), and imaging through the plastic via an inverted? This could be ‘ok’ for brightfield, but will diminish fluorescent performance significantly.
Glass bottom dishes are much cheaper than they used to be (not MatTek), or you can make your own by drilling a hole in the bottom of the 35mm dish and using epoxy or super glue to put on your own slip (did this in grad school) - dirty little secret - you can even reuse them!