Since you have the supercap to support the long power outage, I'm at a loss as to why you need anything close to a 3300uf input capacitor. Am I missing something really basic here? That whole input power section could be cut way down in size, and you should be able to use an LM317T for the regulation.
I do a very similar thing with my TMCC Battery Replacement product, I have an input regulator that steps track power down to 5V to charge a supercap, then that feeds a switching boost regulator circuit to provide 8 volts to the RailSounds battery input. The actual PCB is .8" x 1.2". The whole package with a battery clip is smaller than a 9V battery. The other side has the three terminal regulator, the input filter caps, and of course, the supercap. My filter caps for the input state are two 150uf caps, plenty sufficient to charge the supercap.
