After I bollixed it up before, I sat down and thought about it. The rule of thumb seems to be:
Filter effects (wah, auto wah’s)>Distortion>Modulations (phaser, flanger, tremelo, Ring modulater, etc.)>Delay (includes chorus).
Stage tuners and compressors generally come first or last, noise supressors come last (or are put in effects loops). And pitch shifters are either put before the "filters" or are put in with the other modulators.
So in my brain it’d go:
fender deluxe fat strat —
bionix expandora I distortion
mxr phase 90
boss ce-2 chorus
boss digital delay dd-5
you didn’t say anything about amps. If you’ve got multiple amps you can put the chorus after the delay and get a stereo effect (always fantastic). otherwise, this’ll be cool.