98 with 79k was running good for about a month (about 4 tanks) and then it started running really rough below 5k rpm, the exhaust sounded like one or more of the cylinders weren't firing, and would noticeably return to a more typical tight sound after 5-6k

first time at the shop, they checked the exhaust temps from the cylinders and found one was running lower so they changed out the plugs and took it for a spin to clear out the un-burned gas. Bike ran fine for three more tanks, including mostly highway and track day ridding.

second time at the shop, they checked the plugs, two where running black, so they reset the valves a bit, checked and synced the carbs. that cleared up the plugs and the bike felt silky smooth.

i can't afford a third time at the shop, 'dad says (retired naval engineer) says it's the coils, or plug leads from the coils, should i pickup a pair and try some swapping? would coils show these symptoms and clear up at higher rpms?

most of the time the problem "appeared" the bike had run fine coming out of a garage going to work, then after sitting in the rain / drizzle at work all day, the bike would experience the problem

 

I do hope the shop aren't just spraying carb cleaner down the throats along with quite a lot of starter fluid in the carbs
Your dad could well be right or it could be many number of possibilities
Bad earth somewhere
Regulator/rectifier
PAIR intake
Slow/idle jets or air passages blocked
Etc

You will need to do some good fault finding or hopefully get advise from someone more experienced than me bud.

Good luck
Ride Safe,
Ant.

 

replaced the regulator/rectifier in march when the bike died a couple times, the bike just slowly lost electrical power everywhere, lights dimmed, seemed quite different then this

today was warm and dry so the bike turned over fine first time, but i couldn't get my meter with max & data hold to read the voltage coming out of the coils

 

tried a set of coils from '90 cbr600f, including the wires:
cylinder 4 is still running ~60 deg cooler then the others when the "roughness" starts (measured exhaust right after header)

letting the bike cool down for a bit seems to help, firing it back up an hour later and it takes a couple minutes of letting the bike warm up till i know if the problem is still there or not