Gears digging holes into the filament causing the print to stop halfway through  

You can adjust the idler screw on the extruder and loosen it a bit. All in all, I found the Mini to be very sensitive to the idler setting. I know others have managed to do it, I eventually gave up and upgraded both my Minis to a Bondtech dual drive extruder (the Trianglelab clone on Aliexpress). Haven't had a single problem ever since.

Cleaning

I have had issues with this before. 

Check out your manual on page (3d Printing Handbook 9.9 Extruder Drive Gear and 9.11 Clogged/Jammed Extruder). You can clean the gear with a toothpick or blow air into it to get rid of residue. Below is a better way to get at the gear:

https://www.help.prusa3d.com/en/guide/how-to-access-and-clean-the-extruder-pulley-mini_126457

This one is important as well:    https://help.prusa3d.com/ja/article/idler-screw-tension_177367

Why do I need a "Title" in my reply?

I had similar issues after my first 5-6 prints with PLA.  I followed the manual and took apart the extruder assembly and removed the large gear for cleaning; however, a toothpick would've been essentially useless for me (aside from using it to poke/flick PLA shavings out of the orange housing).  The problem for me was the tiny teeth that are responsible for feeding the filament through the PTFE tubing.  The PLA stuck in these teeth seemed like it had almost been melted into them, and was seemingly impossible to get out.  The instructions say to use a steel brush to clean these parts, but even that did absolutely nothing for me.  I had to use the "acupuncture needle" that was provided with the machine to dig the PLA out of each and every one of these little slots.  It was a pain in the arse and very frustrating, but it worked.  When I had finished this process, the needle was completely mangled.

I then completely removed the tension adjustment screw as well and blew all of these parts out with compressed air.  Then reassembled them per the directions, and set the adjustment screw to be flush with the orange housing (just like the manual says as well), and printed a couple more things with PLA.  Then I found myself in the same position as before: under-extruding filament because these teeth were clogged and the entire assembly was full of chewed up filament dust.  Again I had to take it all apart and clean it.  It was obvious that the tension was still WAY too tight, resulting in the filament getting chewed up.  I removed the screw completely, then BARELY turned it back in - just enough that it wouldn't fall out, but so damn loose you could see it wobbling around if you shook it. 

It has been assembled that way for almost a week now and I've had ZERO issues after probably 40 hours of printing PLA and PETG this week.  Not sure what's going on here, but it definitely seems like the tension screw on these newer machines is faulty.