Dale, are you using the VR that came with the Ron Francis kit? I have one in my 69 RR, using a standard mopar alternator (dual field) and I had some issues with not getting constant voltage. I had it wired as stated from Ron Francis. I did a bunch of research on line and discovered 2 things..
1. the Ron Francis regulator is a SS Ford style (if it's the same as mine, it should look like this
http://www.partsgeek.com/2znktmh-fo...ek+Bing&gb=pp&utm_term=Ford+Voltage+Regulator )
2. It is a great regulator (dare I say better design than mopar) but Ron has it wired in a bad way. The best part about the ford charging system vs mopar is the use of Remote Voltage Sensing. I have a thread here on the forum that went through my trials and tribulations and has a link to a site that nailed how to rewire to use the VR properly. In a nutshell the issue for me was the way RF had it wired was sensing voltage directly at the alternator, which was causing it to produce voltage either over or under the needed amount elsewhere in the system (like at the dash gauges, headlamps, ect..) the key is to wire it to sense voltage at a centralized junction point, equally distant as far as wire runs, from all of the major items, which usually mean somewhere close to the firewall bulkhead conn (which you probably don't have if you have a RF kit like me). I have a positive power stud mounted to the firewall that I run main power to most systems from... s, 4 feet to batt, 6 feet to alt, 4 feet to dash, ect.. this is where I sense the voltage to control the regulator.
The benefit is that it reduces the voltage drop over long runs of wiring that will cause the regulator to over or under produce. BTW.. Once I made this change, the voltage now appears +/- .3V almost everywhere in the car!
One other major component of this issue is the resistance value across the wiring/connectors, so make sure you have good clean connections and good crimps.
BTW, I have an MSD 6A, MSD dist as well.
Your 100 amp alternator should be fine, as the system will only use the amps it needs.
I know I might be shunned, but mopar's charging system and wiring are a weak link in their design compared to GM/Ford.. If you don't mind non-orig.. stick with the ford style VR, just wire it to take advantage of the remote volt sensing and it should work better than stock.