Honored Contributor
Honored ContributorWhoa let's not make this too complicated. If your grounds are seperated with no way of making them common, then yes your best bet is to run differential. If your grounds are not related to each other in some way, then you have absolutely no way of knowing what the potential between the two is.
However remember we're only talking 40Mbps here. Run four traces (a differential clock and a differential data signal). Use AC coupling caps on the traces (preferably close to the receiver). And use a simple DC-biased termination scheme. If you provide the clock, there is absolutely no need to encode the data. Encoding schemes like 8b/10b are designed to provide a maximum number of transitions to allow for easier clock data recover at the receiver. Just provide the clock. I assume that your boards have been layed out with differential traces? Jake
