So i then hooked up the multi meter to the same plug to see what the voltage is in all 3 legs, I came up with 4.8 volts on each leg which should add up to 14.4 volts. So somewhere between the r/r and the battery I'm loosing volts. Now what?
Not sure you quite understand what is going on, here. Your statement of three lots of 4.8 volts adding up to 12.4 has no meaning in this context, these voltages are not added in that way.
Was your meter set to measure AC or DC?
If AC, 4.8 volts is very low.
If DC, you should get near enough zero volts, are you sure there wasn't a little "m" in front of the display's "V"? That would mean millivolts.
Set the meter to AC volts. With the engine at idle, you should read something like 20V between any pair of the three connections. At 5000rpm, it's something like 70 volts (these are from memory).
All three should read the same (within a few percent).
One other check you should do, make sure there is no connection from any stator wire to the bike's frame. In the same way that you measured the resistance of a stator coil, measure between one of the connections and the bike's engine or frame. It should be open circuit (meter will show something like "oL" (overload), the same as it shows with the probes not connecting to anything, although it is possible your meter will show a very high reading (10M or so), this can be ignored.