Did you get the owners manual?
There is a routine maintenance schedule/list in there.
Sounds like you need to check points and timing.
For me, if I don't know what parts of the tune up has been completed or when, it is due now. And, it is certainly the first thing to be done whenever the bike begins to run poorly.
The order of parts replacement is important, too. If the plugs were fouling, then replaced, and later the air filter was replaced. It may have been the filter fouling plugs, which were sooted up by the dirty air filter.
Having said all that, the voice of doom says that this model of bike often had valve guide wear issues. I would probably put the compression test first on the list. If the compression is bad, tuning ain't gonna fix it!
FYI, taking out the baffle likely requires a change in main jet size, to compensate for the increased noise the bike makes. In essence, you took power away from the engine with that change. You may also need to change the slide needle position. A new filter with less restriction would have made the bike even leaner.
Time to learn to read spark plug deposits and how the carbs make the proper air/fuel ratio.
