OK here goes. It might help to look at the bit I wrote about electronic ignitions elswhere in this section. I can't tell you how this hooks into the MSD system as I don't have one but this is how the stock ignition should hook up.
Disconnect your battery.
Remove your old ballast resistor and fit the new one in it's place.
Look at this diagram
it is the view of the rubber plug that fits onto the chrome box. I did the drawing so that it is the same as looking at the contacts inside of the plug when you pull it off and turn it over.
There should be two wires coming off pins 4 and 5 that go to the connector on the distributor yes?
Take the (green?) wire from pin 3 and cut it off.
The wire from pin 2 should go to the negative of the coil.
Pin 1 is connected to one end of the ballast resistor.
The coil positive should be connected to the other end of the resistor.
Now we have to sort out the remaining wires (the tricky bit).
I don't know how many wires you have because sometimes they are connected together elsewhere before they get to the resistor so you need to check with a meter to see where they connect to.
But you want the alternator field, voltage regulator, and the wire coming from ignition 1 (run) connected to the same side of the resistor as the wire from pin 1 on the connector.
On the other end with the lead from the positive of the coil you want a wire from the other position on the switch (ign 2) which is the position when cranking the engine. This may be a brown wire.
Also make sure you have a good connection between the chrome box case and earth.
I hope this makes some kind of sense.