i've taken all of those bus/train routes that you mentioned many times. if i were doing what youre doing, i'd just box the bikes in chico since you'll have to do it eventually anyway. it eliminates any problems that might come later in the trip. that's alot of transferring and it just takes one cantankerous driver to leave you in a bad situation. chico to bakesfield you'd have no problems at all (most likely) but the bus from LA to bakersfield will probably be packed full of people. with the bikes in a box, they'll take up alot less room and make it less likely that they wont fit or that the bus driver wont just be pissy about it and not let you put them on, because that CAN happen sometimes!
edit: on the san joaquin train they MIGHT want you to check the boxed bikes in, but i've never been charged for it. usually they have the lower level of one of the cars reserved for this sort of thing and i've never had a problem.