+1 to widespread
If it is Nylon, chances are you will need a toothbrush or something similar. However, most PLA and ABS shavings can be blown off with air.
Before you have a full blown nightmare, print a new extruder. The MK5 is proven to work with the stock PEEK hotend and makes maintenance much easier. I know you have been having issues with your machine, and if you put this off, you may eventually break the acrylic and napalm your printer. Better to have it and not need it.
Also, When switching between filaments, if one is significantly larger than the other (0.1+/-) you want to adjust your tension arm. If your extruder is expecting a smaller diameter, too much material will be forced down and eventually jam. You can make all the software adjustments you want, but the spring is just a spring and cannot be commanded on what to expect. Too much tension will cause the drive gear to chew through the line....I think this may be the cause of your current dilemma.
Printit Mason and Printit Horizon printers
Multiple SD2s- Bulldog XL, E3D v5/v6/Lite6, Volcano, Hobb Goblin, Titan, .9 motor, Lawsy carriages, direct Y drive, fishing line...the list goes on
Filawinder and Filastruder #1870.....worth every penny!