Current status summary based on my understanding: The starboard side motor was showing signs of hesitation prior to the carb rebuild, now runs well (unsure if problem was corrected and if yes, how).
The port side motor is now not running correctly, only maybe 30% power.
Sounds like a dead hole. Could be a dry carburetor, which also means potential lack of lubrication due to lack of fuel to distribute the lubricant within the dry cylinder.
I'd pull the plugs and reconfirm compression, may be no damage if the motor wasn't run very long with a dry hole. If there's any doubt, shoot some lube in the cylinder in case it's dry and mix up a squirt bottle of pre-mix to fuel the suspected dry hole, then see if it pops back to life by squirting some fuel mix into the carb.