If your electrical system is already struggling under the load that your giving it.. doing a cap isn't going to help at all. If the alt can't already keep up with charging the battery AND running all of the electrical systems AND your system, and then you add another item that it has to charge.. like a cap, then you're basically screwing yourself even more.
What I would suggest.. is talking to some alternator shops and seeing if they can build a custom bracket for your vehicle. Nate at Excessive Amperage is going to modify a 200 amp alt for my car for $270. It's not for my vehicle, but the ONLY thing thats not for my vehicle is the mounting bracket, and he's going to make it work. That, my friend, is your best option at this point... and do the Big Three as well, as it will help facilitate the flow of electricity to your major electrical components.