A reg/rec can have two ways of figuring out how much voltage to output. The older style use a sense wire, usually from the brown circuit and this wire will show voltage on that circuit and the reg/rec will adjust. That is the way the original separate regulator and rectifier worked. Newer style reg/rec units derive voltage sense from the WHITE wire (might be white with red stripe) going to the battery and fuse box after a split. Older reg/rec units had a BLACK wire which is a ground. The three yellow wires are coming from your stator and supply the A/C voltage.
Your panel arrangement will have little to do with the connections of your new reg/rec directly as the circuits come off the fuse block that is powered by the white wire from the reg/rec. I highly recommend heading to the auto parts store and buying a small modern fuse box using modern plug in style fuses. You can un-solder the orignal wire leads going to the junction thing where the plugs are and solder them into the new fuse box. Much better chance of good connections at this point.
Texas Hill Country