As you're probably aware you're basically looking for where the voltage drop is occurring. If you have 12 volts at the battery and 10.5 at the terminal block under the dash somewhere between the two points you're dropping 1.5 volts. Running temporary wires for ground and hot (one at a time) and checking voltages for change will tell you which of the connections is having issues.
Like wise eliminating circuits and checking voltages will help in determining if you have a short that is drawing down the voltage. I've heard that bad diodes in the alternator can cause some weird electrical issues but it sounds like you've already eliminated that.