That choice is an ok unit, I might upgrade to a set with a different coil. That coil has molded in wires. If a wire goes bad it's tough to fix. I might suggest #14-0912. I bit more costly but it uses a coil that you can easily change wires.
The Pamco doesn't run the Pamco. It's only an ignition it just sparks the plugs.
The PMA is just an alternator, it makes electricity to run the bike and charge a battery. Unless you aren't using a battery. Then it just runs the bike.
The Pamco only needs the proper voltage to work. It doesn't really care where it gets the voltage.
I would install the Pamco into your bike now. Run it for awhile to ensure it is timed right.
Once you get it set up and running install the PMA. Now to test the PMA, hook the Pamco to a battery by itself. Hook the PMA up to the rest of the bike. Run the bike, test the PMA for proper voltage. Once confirmed then hook the Pamco to the bike.
If you just install both the Pamco and PMA the PMA may have issues that send voltage spikes to in excess of 20 volts. This can damage the Pamco.
Test things out as described and this will be not such a problem.
I might also suggest adding a volt meter to your bike. Somewhere easy to see. I have mine mounted to the handle bar risers. This will tell you, you have voltage issues before things get damaged.
I recommend this for all bikes. It just might save you pushing a bike home, or calling for a trailer.
Leo