I love this DISboard!! It is making me even MORE excited about our vacation! We are arriving in 18 days and counting.
I was wondering about transportation to other resorts? How does that work? Do you have to take the bus to a park, and then catch a bus from there to other resorts?
Yes, you need to take a bus from your resort to the closest park and then catch a bus (or the monorail, or even a boat-depending on which resort you are going to). We are dining at Jiko one night, and Kona cafe another.
For Jiko, I would suggest taking a cab. CSR is not that far (or so I've heard) from AK, and AKL is pretty much down the road. But, if AK is still open, take a bus to there and then hop on the AKL bus. Just make sure you get off at the stop for Jambo House, we made that mistake two trips ago and walked forever to get to it! For Kona, just take a bus from CSR to MK and hop on the monorail to the Poly. 
We are doing a charater breakfast at CBR one morning, but will be taking a cab as suggested on here before. We do have a toddler who needs a carseat in a car...anyone have experience with toddlers and cabs at Disney?
Unfortunately, I can't help you here. I'm guessing they just expect you to buckle them up between you??? But I have no idea.
Also, does anyone know during the busy time(that we are in Disney) how long should we allow for travel between parks, or from parks to resort if we have a reservation?
They usually recommend to allow for one hour for travel. Some take that long, some don't. It really depends on the buses. If you can figure out the carseat and taxi ordeal and can allot some extra case for a taxi, I would definitely suggest taking a taxi if you feel you would be pressed for time. Just a suggestion to take a stress off. DH and I are going in October and for breakfast we are definitely planning on taking a cab, that way we get 30 more minutes of precious sleep time and don't have to worry about racing to our ADR to make it time, if the need should arise!
Has anyone taken the bass fishing trip offered at CSR? Might be silyl to think of bass fishing while at Disney but it might be a nice change of pace for my husband and teenage son. How about the kayaks..worth renting?
Sorry, I can't be of any help here. I would love for my DDad to come to WDW with us and go fishing, as it is his favorite!