I'm trying to thing of the best way to explain this scenario...
If you decide to take the Coast Starlight it would be to your advantage to book earlier in the process as that train is based on a "bucket" system. Basically that's the Amtrak version of Supply and Demand Pricing. The more people that book, the lower the available inventory, thus the price goes up accordingly when the inventory hits a certain level.
If you book using the bus-train-bus route, the price is generally fixed. The Capitol Corridor Joint Powers Authority sets the Capitol Corridor fares based on a fixed pricing table. The fares will only change if there is a scheduled permanent fare increase across the board.
With that said, the price may go up a few dollars as the bus connection is a Thruway route that is scheduled to connect to the San Joaquin Route which does use bucket and holiday pricing. That price on the bus segment of your trip may change but only by a few dollars at most, mostly during the peak and holiday season.
The main concern would be in terms of space on the bus from CIC-SAC. That bus generally does not sell out, however it is reserved meaning that there are a fixed number of seats to be sold. Given that your trip is well in the future you shouldn't have an issue in that regard either.
Only things to remember are Amtrak allows bookings up to 11 months in advance and you need to book at least 3 days in advance to obtain your AAA discount of 10%. The train and bus from EMY-SFW are unreserved on most schedules (all CC trains are, most buses are) so if you decide to spend some time in Sacramento or Emeryville or for some reason your plans change along the way, the unreserved segments are valid for one year from the date of issue. Keep an eye out for discounts that may pop up such as the winter 20% sale or AAA 10% + 10% sales that are currently going on. These may occur again next year during the time you are traveling so you may be eligible for a larger discount depending on the terms of the sale.
As for refunds... Amtrak has recently changed it's refund policies. Unreserved trains are refundable, minus 10% of the fare paid. You may also obtain an "E-Voucher" which is for the full value of the ticket and valid for up to one year from the date of issue. Since the first segment of your trip is on a bus, you should be subject to the "Reserved" train policies. Your reservation is refundable for the full-value up to one day before your departure. After that, or if you no show, you will be issued an E-Voucher valid for one year for the full value of the fare.
This by no means explains all the rules or scenarios and I'm sorry if it is a bit of information. Bottom Line, if you do the bus-train-bus combination:
1. There is no real advantage in your case to booking early and if you do, keep an eye out for specials that may come along.
2. Your ticket should be fully refundable up to one day in advance of your scheduled departure as long as you have a reserved portion in it.