I'll take a stab at this. If you haven't found any resources after a thorough google search, I'd say you're stuck with just opening up the API's of each and just consulting them back and forth and looking at the examples.
I'm actually going from Prototype to jQuery on a project right now. (Aside: I'm much happier with jQuery having used both for awhile.) My basic work flow is just referencing the API as needed.
I would be surprised if there was such a mapping of one to the other though. In either framework, there are many ways of doing any given task, and on top of that they work in different and important ways. Sure there's some 1:1 correspondence like "addClass" vs. "addClassName", but jQuery DOM manipulation typically works on sets of elements (which may be just a set of 1) while Prototype works on single elements (which may be wrapped by an each statement to work with sets).
Fortunately, both have pretty good and easy to use/reference API's.
Good luck.