Okay, I managed to figure out the problem. It was a combination of adjusting the Z switch, and clearing out small bits of filament stuck on the hobble wheel. When I took the extruder apart, I found that the grooves in the hobble wheel were filled with small pieces of filament, and that meant that the filament was slipping.
So, after clearing that out and resetting the Z level adjustment, no more clumping and the test print is nice and smooth.
However, I think this was caused by a design issue in the printer. The Pronterface software stops the extruder from extruding when it is cold, but the built-in controller doesn’t. So, what I think I did was to accidentally start a bed test print (which does not include commands to pre-heat the extruder and bed) without pre-heating the extruder. This meant that the hobble wheel was chewing away at the filament, which couldn’t go anywhere. Instead, it just gnawed off bits of filament and got clogged up.
My suggestion from this would be to either add pre-heating commands to the bed test print (and then create one for ABS and one for PLA), or add a check in the firmware that prevents the extruder from extruding when cold.
TL:DR - If you are getting globby, clumpy prints like mine, clean out your extruder and check your z height adjustment.