Prusa i3 MK3S keeps clogging during print. Ugly streaks sometimes, and complete clog when printing with lower layer lines
My problem was 2 things. The heatbreak, which was switched out for the MK2 version(Explantation below). And the Teflon Tube that runs down the heatsink.

Heatbreak

Change the heat-break to a generic E3D one. You can order the heatbreak for the MK2 from prusa, or any generic heat break for the E3D hot-end assembly.

On the Prusa i3 MK3(s), this component has been given a 45° taper in the middle, between 2.2 and 2&nbsp;mm. This is done to ease filament retraction for the MMU, and will be nothing but problematic if you are not using the multi-material upgrade. Especially with higher nozzle pressures(eq. with lower layer lines), the filament may be squeezed into this taper, clogging the hot-end.

You may not experience full clogs, but partial ones that will show themselves as streaks in certain layers on the print.

Heatsink Teflon Tube

There is a teflon tube that runs down the heatsink. It's crucial that this is mounted correctly and it is not entirely intuative how.

First, press the teflon tube into the heatsink all the way to the bottom. Then, try to pull it out slightly. You'll notice that the small plastic ring at the top of the heatsink will pull out slightly along with it. Now, hold this black plastic part at it's current position with your fingernail, and push the teflon tube in the extra amount. When done, there should be no play in the tube.