I agree with the posters about taking the Amtrak. I'd also add that when you ticket your journey, call (instead of online) and tell the rep that you will need disability assistance. They then will have a little extra time to help you board (the San Juan Cap station is a quick on-off station).
BETTER YET, spend the extra $15 and ride in the Business Class section. You get extra service in that car (free beverage, and for the cost of the food, they'll bring you something from the snack car [you may have to specifically ask]). The seats and seating arrangement will be a lot more comfortable. If you do choose this option, you will board the train car that is closest to the forward engine (it will stop close to the parking garage). If you travel regular class, you will board toward the rear engine (down the "platform" closer to the restaurants). I live in Dana Point and my mom takes this trip all the time!