I am using Slic3r Prusa edition with the default settings recommended by Prusa for their MMU, this means 4mm retraction length. I don't want to mess around with those settings, because they should be ok for the filament they tested on their printer.
Printing speed is 40mm/s for perimeters and 60mm/s for infill.
Enclosure temperature (the time I monitored it to see if it would clog again, which it did) was 29 degrees. I don't know how much hotter it would get if it continued as I don't continue printing once this happens. I don't think it's the highest temperature it would reach.
I presume I need to work on the air flow. The issue with the filter I printed is that the fan makes a huge amount of noise when going full force, which defeats one of the purposes of the enclosure, being to reduce noise levels when printing during the night :D
I'm going to install a dual 120mm extraction setup with some high pressure Noctua fans behind a carbon filter/HEPA filter setup. Hopefully this helps whilst keeping the noise down. Will drill some extra holes at the bottom to get more air in the enclosure too.