Ender 3 Pro Extruder Stepper Skipping with a Chunk sound
UPDATE 3-May-2020: I have now confirmed that the problem was the extruder. Specifically, the input port which was causing the filament to bind. The front of the input port is a metal ring but the back is just plastic and and has worn from the PLA filament, as seen in this photo:

After some delay (see my other question here) I have installed the new, all-metal extruder (original stepper), the clacking is gone as well as the significant under-extrusion. (I also replaced the Bowden tube and print bed springs but I don't believe these were the problem).

Having seen what a few km of PLA did, I highly recommend upgrading the extruder.

Side point: immediately after the replacement, I started getting corners lifting off the bed which I hadn't seen before. I realized that the new drive gear was slightly smaller than the old so I checked the extruder calibration and it was about 10% low. I adjusted the extruder steps/mm from 93 to 99 to correct for this.



Original:

It appears the problem was the filament binding in the entry to the extruder assembly. I did start seeing signs of under extrudement such as the outer layer of a rectangular object separating of the rest of the body. Later, the problem became worse, with a lot of clanking, to the point that prints became quite fragile.

I have ordered a all-metal extruder assembly and will update as I get new results.

By the way, I'm really not sure why it's binding but running a strip of filament through the entrance hole, it sure seem to be binding. But in trying to disassemble the extruder and starting by removing the filament, I managed to get molten filament in the bowden tube. Without thinking about it, I pulled the blob all the way into the fitting for the extruder, plugging it so much that I cannot get the fitting off nor push it back into the tube. Anyway, I'm taking the opportunity to upgrade the extruder, tube and springs.