Please don't use low quality paper towels when cleaning the inside of your printer, especially the bottom of the print head, because as you've experienced, they fall apart and cause problems....
I recommend getting a roll of high quality paper towels, such as Bounty White (NOT Basic), and carefully cleaning your print head again.
Have you been making any prints, or just doing a lot of cleaning? How do the physical ink levels in the carts compare to the status monitor levels? Does ink seem to be dripping from any channel when you make prints, or are you just having the opposite problem of missing nozzles?
Please let me know, thanks~ Dana