Capacitors for audio applications tend to run $80+, and are just a bandaid. Half the time, they do nothing...
Your problem is obviously the alternator. 35 amps is weaksauce. It was designed strictly for keeping your boat running, and nothing more, as it doesnt need turn signals, headlights, brake lights, etc. etc. A normal car alternator puts out 50 amps and up, and they are quite often not enough for a high output stereo.
I suggest looking around to find a place that will rewind your alternator. They can put different parts into it, and wind it tighter, to produce more power. They will also put new contacts into it to make it last a lot longer. This is also way cheaper than buying a whole new alternator, and may even be cheaper than a brand new capacitor.
BTW, this belongs in the TECH section.