Don't forget that if you use a CANJaguar, you can use the encoder directly attached to said Jaguar. My team has successfully done that in the past.
This year, I'm using a
AMT-102 capacitive encoder, which I like a lot better than the kit ones. Adjustable lines/rev (48-2048), mounts on just about anything up to the size of the CIM shaft without machining, and it seems to be more reliable than optical encoders IMHO (don't have much experience with magnetic

). Also, it has an index count (aka one pulse per rotation on a separate pin). Worth a look at least.