The new PTFE tube that came with the MMU2S kit indeed has bit smaller ID so I swapped it in the extruder. Luckily the current Prusa extruder is actually quite easy to dismantle enought to get to the hotend.
After swapping the tube the print finally finished without jams, although the MMU2S unit needed some attention couple of times; seems that FINDA didn't trigger when pulling filament out or something. Probably need to adjust it slightly.
Dissolved the BVOH overnight, most of it was gone by then. However, some bits were left that didn't dissolve and had to be removed manually. Probably had some PLA in them because I didn't have enough purge for materials to be fully purged and there's some mixing happening. In previous tests, BVOH needs to be purged at least 80mm, otherwise it starts to affect PLA and especially PETG strength.

IMG_20200929_143928.jpgIMG_20200925_185127.jpgIMG_20200929_143912.jpg