Disclamer: Keep in mind I've never installed this kit. I'm no expert and I'm not responsible for your engine. This is just what I'd do if it were mine.
I was doing some checking for you. My info is all comming from the pertronix web site and the July issue of Ol' Skool Rods magazine. Are you sure you can remove the ballast resistor? Did the instructions say to do so? Check out the instalation instructions on Pertronix's site: http://www.pertronix.com/support/manuals/pdf/billetvw%20Ignitor.pdf
I know that guide is for one of their billet distributors, but I'm thinking the same thing applies to your coil. Now take a look at this: http://www.pertronix.com/support/manuals/pdf/ignitor12vneg.pdf That should be the instructions to wire up your ignitor, it also mentions keeping the balast resistor. It even has a handy little diagram that shows the balast resistor all wired up.
Here is how the stock wiring is setup:
The ballast resistor isn't wired directly to the coil, there SHOULD be a black and white wire that comes from the ignition switch connects to the ballast resistor which connects on the other side to a green and white wire that goes back to the tach then comes back and connects to the positive side of the coil. There is also a green/blue wire that bypasses the resistor and is only 'hot' while the car is cranking.
With that in mind, I'd put the ballast resistor back in and connect the new red wire for the ignitor to the black and white wire where it connects to the ballast resistor (as per the diagram in the pdf). The black/white wire that was connected to the original coil on the positive side should still be connected in the same place. Then I'd connect the new black wire to the ignitor to the negative terminal on the coil.
All in all I think it should be pretty much like stock except you add the red wire to the ignition switch side of the balast resistor (black/white wire) and switch out the black wire that connects to the points distributor for the new black wire that connects to the new ignitor. Make sense?
I can add clarification if you need, but if you still have questions it's a good idea to call Pertronix. Their number was on their website: 909-599-5955.