The “stumble” issue could be a number of problems, but it looks like your bike is a 1999 or 2000 model judging by the 220mph speedo.
It’s helpful if you offer info re model year and mileage on odometer for any sort of advice needed.
This particular model has an external fuel pump which is prone to clogging filters and overheating causing cavitation.
Without proper maintenance (as you’ve admitted) your bike WILL give trouble and the fuel pump is no exception.
So, it’s ( fuel pump) going to need a full strip down, clean out, and new filter in the pump at the very least.
There are a few threads here re external fuel pump strip downs so use the search function to find that info.
There are also online manuals available here on the org, ask
@Berlin Germany for a link, I’m sure he will be happy to help AND to give you a few choice words of advice re manuals.
As for the clunking noise, be sure to have the idle speed set to 1200 to 1300 rpm.
Also, if the noise goes away after you pull in the clutch while idling, it’s a noisy clutch.
Other possibility is the the clutch pressure plate bolts are loose and dragging on the inside of the clutch cover.
Need to remove the cover to check for scrape marks and loose bolts.
Welcome along, please post up more pics of your Busa!