Fellow microscopist here. You should look into building an IR focus lock onto your microscope. Basically, you reflect an IR beam off the coverglass such that the xy-position of the reflected beam tells you about the distance from the objective to the coverglass. You can then use this information (read out w/ something like a QPD) to feedback into an automated piezo stage to automatically correct your focus throughout long imaging runs.
There is technically an autofocus feature already built in to our system, but I don't know how to use it! I have, in theory, been shown how to use it, but I am only a rotation student and that's it, I'm done, this microscope and I have finished our relationship.
Only being in a lab for 10 weeks = learn to live with some limitations.