Parasitic loss is not a terribly common problem and can be difficult to track down, but luckily the troubleshooting is usually straight forward.
1.) Grab your multimeter and set it to read DC voltage. Then disconnect the negative terminal of the battery from the ground strap (or equivalent).
2.) The everything switched off, read voltage between the negative terminal of the battery and the cable you just disconnected from it. If you get around 12V, you have a parasitic loss. If your reading is only very small fractions of a volt or you have no reading at all, then the problem is the battery.
3.) We're going to assume you have a parasitic loss and continue the troubleshooting. Nine times out of 10, the issue is with the regulator/rectifier. As a quick test, disconnect it from the harness and repeat your measurement from step two. If the voltage loss has gone away, it's time for a new R/R (assuming it's wired correctly, that is).
4.) If the R/R wasn't the problem, it's time to start following all of the wires and cables you may have connected to the positive battery terminal. Start disconnecting things one at a time (followed be repeated measurements) until you find the culprit. The underlying issue might be something hooked up to power from the battery when it needs to be hooked up to power after the main switch.