"cylinders 2-3 had reverse polarity off electronic ignition, so he put points back in..."
sounds weird, if the wires were reversed that is not polarity, and if he put in electronic ignition did he get a spark or not

hard to imagine he didn't get a spark, hard to imagine it can't be made to run as stock too.
Have the valve clearances ever been adjusted? They need to checked if it does not start well or changes when it gets warm, that makes it suspect. No matter how nice the bike was cared for the valve clearances would be off by now. That pretty much goes same for all honda engines.