"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.
You live in Canada and you are worried about a motorcycle dealer fleecing you to service a half century old Honda?
Don't worry, if you found somebody willing to service it I guarantee they will fleece you.
CB350F has 180 degree crank offset between cylinders 1&4 compared to cylinders 2&3
they have 2 coils and the 2 sets of points run off the crankshaft with a firing order of 1-3-4-2 so it has a wasted spark.
The only way you could mess that up is to connect the wrong coil to the wrong plug.
Battery fully charged <- tells us almost nothing at all, what kind of battery, is it stock and when was it full charged, when you started out, or most important after it quit on you?
Idle pre-ride was not stable, 1200 - 2000 oscilating, slightest idle screw movement had significant impact <- that sounds like it is running out of fuel. So yes the bike was "tuned" badly if servicing carburetors is called tuning.
Sounds like the bike still has points ignition so it has condensers and those should be replaced if there is any question about the intensity of the spark on the paired cylinders (cylinder 1&4 share one set of points and condenser, cylinder 2&3 run of the other set, so compare the spark between each set to determine if only half your ignition system is running great)
The bike runs a battery and coil ignition system, she won't run without a good battery and the battery will die if it is running on dead loss without being charged, so you should be checking the alternator and charging system.