Note that the brass toothed gear can also wear out. Maybe check it to see if there’s a lot of ground-up filament in the teeth? Then check the fitting where the bowden tube goes into the extruder, make sure that isn’t loose (it will be seen moving back and forth during retractions in a print). Also worth checking the bowden tube itself, make sure it’s not causing a lot of drag on the filament passing through it. And for that PTFE mod in the hotend, check the friction there, it’s possible to over-tighten the fitting and partially crush that tubing. You should be able to easily push filament through the hotend by hand once it is up to temp.

I assume you have something other than the stock setup for your filament roll to reduce the drag there so it’s not being pulled into the extruder at a 90-degree angle? There are a number of extension arms you can print to change the angle, but the best methods are either to move the filament spool off to the side (where the filament can enter the extruder in a straight line), or print a roller that uses a bearing for changing the angle in combination with a full bearing-supported roller that the filament spool itself sits on. I still have mine in the stock position on top of the frame but with the combination of bearing objects in the last option I have practically zero friction pulling the filament into the extruder.

Finally, when was the last time you calibrated your E-steps? It’s likely you actually have underextrusion on all layers, but they’re getting smoothed over and are not as obvious on the alternate layers. Never hurts to check this step.

tl;dr: eliminate all friction from the spool to the hotend, calibrate E-steps.