You can order direct from Yamaha, through their website. If you have trouble finding the correct part number, just send them an email and they'll help you out eventually. Sometimes you need to send repeated emails though. I've purchased quite a few spare parts direct.
You need to create an account first. Then once you're in, just search the part database using the model number. For example, if you enter DFP (for double foot pedal), you'll get a bunch of suggestions in a dropdown, then you can click on one of them, then click "GO" and you'll be presented with a diagram that shows all the individual parts and their numbers, along with a list of the parts, and the ability to add them to your shopping cart.
Keep in mind that the prices for parts are kind of high. For example, one of their bass drums beaters for the newest generation of their pedals is about $50. Other stuff is more reasonable.