I had replaced my original harness which was in a bad and cut up shape as well.
On the side of that i run any additional wiring for the MSD ignition and other extra's i added to the car.
Once the standard harness is in place you can use it to support all additional wiring you require.
Once tested and all is good, label and disconnect everything and wrap the extra wiring to make it look like stock.
I think all these harnesses you can buy that are "so easy to install" are just a PITA, you can add additional fuse boxes, relais as you like, just make a good drawing and pick a good location for the components.
As rmchrgr said, for the MSD you can use the IGN1 and IGN2 wiring for a full 12V source, the MSD's do not require the use of a ballast resistor.
I used these together to function a 40Amp relais to provide a full 12V source direct from battery to the ignition to relief this electrical load from the main harness.
You could do the same if you plan on running H4 type head lights as an example to keep those heavy loads of the main wiring.
And don't forget to include a new firewall connector, the old one will likely be in bad shape and can cause problems.