I thought that I had seen somewhere about changing a transponder code on a ship to kind of "hide its identity". To keep the game moving, I made it a Daunting computers check on the fly, but I was wondering if there was anywhere that had an actual reference to this in the CRB or am I perhaps thinking of an older edition?

Also, where in the CRB does it talk about co-op skills, like giving aid to another person. I seem to remember that if you have different ability dice and proficiency dice pool, then you take the highest of the ability and the highest of the proficiency, but I'm not sure if that's exactly right.

Yes, the cooperating rules work exactly like that - highest characteristic and highest skill. If the same player has both, add a boost die for the one helping him.

The old D6 system had rules for changing transponder codes, but I can't remember seeing anything in the core rules about it. The basic rundown from the D6 system was to first browse the BoSS database for a ship of the same model with an approximately similar code, then program your engine to transmit that code on top of your own, bleeding the signals together. The more codes you had installed, the more obvious it was that something was fishy. I'd make it a Knowledge (Education) to browse the database (difficulty depending on how rare or common your ship is) and a Daunting Computers for the first code, Formidable for the second, and then start upgrading.

Thanks for your help!