If your serious about the bike bring it home and do the work yourself. A"shop" will bleed u dry. The 650 isnt that hard to work on. But it is a 30 year old and probably needs help. And every bike has issues after that time and previous owners.
That being said the bike has 2 ignition circuits on 1/4 and 2/3 cyls. So it might be carbs. Hows the tank inside? first place to start no matter what in my small book.
I agree withe everything cb650 said.
The carbs have been cleaned and checked 3 times the gas tank looks almost new. The bike is super clean everywhere.
It doesn't matter how many times they have been cleaned if there is fine particulate getting into them plugging them up again.
Disconnect the fuel line from the carbs, turn on the petcock, and allow some gas into a clear jar. From that you will be able to see any debris that may be getting into the carbs.
The only way it would be ignition related with 1 & 3 being the problem is if the shop in question put the plug wires on wrong. As stated, 1 & 4 are on one coil and ignitor and 2 & 3 are on the other coil and ignitor. If the shop can't get firing order correct, I certainly wouldn't trust them to a carb bank clean and setup correctly.