In dyno testing I have found that a Pertronix does act like a rev limiter, reducing power noticabley in the upper rpm. This is usually around 5500 rpm but yours may be coming in early. More on that part later.
It sounds to me like you have two separate problems, the first being a bog/backfiring issue at lower/medium rpm (right at the shift recovery rpm into second gear or about 3500 rpm) and the second, the engine breaking up above 4800 rpm without backfiring. Is this right? Or can you tell at this point?
Okay, try this test: with the car in second gear bring the engine rpm to 2500 rpm and let it stabilize for a couple seconds then press the pedal down at a medium rate. Do this several times, increasing the speed that you get the pedal to the floor until you are essentially stomping on it. Does this result in the bog/backfiring that you're talking about? Does it get worse if the engine rpm is lower? Do you feel that the engine bogs as soon as the pedal moves or could you feel it more once the pedal is past halfway to the floor? This is testing how well the carb is handling the transition from light load to heavy load at different transition rates.
The second part that may be confusing the issue is the breaking up at higher rpm. To test this, start your testing at 4000 rpm in second gear, again letting it stabilize for a few seconds then getting on it. Concentrate on what is happening at the 4800-5100 rpm that you mentioned before. If the engine is still breaking up at the same rpm each time with no backfiring, then it is very likely that it is an ignition problem, possibly because of the Pertronix. If it doesn't break up, lower the starting rpm and try it again, repeat until you are starting below about 2300-2400 rpm. If you have the appropriate roads do this test in third gear. Watch your engine temp during the test and if it starts cutting out earlier (bog) than it did when starting at 4000 rpm, get out of the throttle, you're running very lean! This is testing how well the fuel system is working to keep the carb supplied with fuel, and also whether the ignition system is limiting your upper rpm. As I said earlier, a fuel pressure gauge in your line to the carb will also show whether the fuel system is keeping pressure to the carb during this kind of test. If you have it, bring a friend so they can watch the gauge while you drive.
The essence of good testing is to be able to repeatedly make the car have the problem with the least amount of other things happening at the same time. For instance, if you can make the car bog without having to rip through first and hit the gear change into second, that can eliminate several other possibilities for the problem. Make careful notes as to the results of the tests, it's very easy to get things confused after the tests!
It should only take about ten minutes to do these tests and you'll have fun at the same time! If anything is unclear just ask!
