You should have no trouble just swapping out the carb. The Pertronix I is a very good upgrade for relatively little money. Think about getting the Flamethrower coil too. Then you can run colder plugs and open them up to .50.
UNLESS the dist is for a load-o-matic, which will cause serious running problems. I have never had this prob and don't know how to identify the load-o-matic distributor system. In that case, you have to get a load-o-matic specific carb. Other guys will help you identify it.
If you don't have the load-o-matic, do the mods in steps. Change out the carb first and get it up to spec. At the very least, you need a vacuum gauge. You really need a dwell tach too. Put the car in 'drive' or neutral, adjust the idle to about 700-750 rpm on the dwell tach. Use a vacuum gauge and adjust the idle to 18 pounds minimum first. Then set then the timing and the fuel mix while the car is idling. You can play with the timing by driving according to the instructions Pony gives you.
Once the car is working well with the new carb, change out the ignition to the system you want to install, in your case the Pertronix. Once it is in, you need to do all the adjustments again. It will be easier this time. First off, you will probably have to back off the idle. You can lean out the fuel mix too, because you have much more efficient combustion with electronic ignition. Then you can fool with the timing as you drive.
This link was useful to me:
http://www.geocities.com/rustobucket/Mu ... nix-1.html
Remember, the Flamethrower is a 12V coil so you have to bypass the 6v pink wire.
If you have more money or time, you might try the DuraSpark II system. These can be salvaged at junk yards or bought new. Read about it here using the 'search' function: DS II is the most common abbreviation. The most expensive but most elegant is the DUI sold by Mike at Classics Inline linked above or the Ford Six Shop below.