@Karlosw , you've already done what I would've suggested to get rid of those black marks on your cover. Cut them buggers off!
Despite what others have said to remove the cover - I think you should keep the pool covered during SLAM. I know it introduces another element in the fight but it's a normal & essential element in your pool equipment so might as well deal with it as such. It might extend SLAM another 2 or 3 days but at least the cover is getting dealt with along with all other elements.
Try to keep the cover submerged while SLAMming as the higher chlorine will deal with hidden nasties. The fact that you managed to semi-submerge it and give it a scrub on the top surface is pretty good. It's hard but can you invert the cover and scrub the underneath?
With a night test at 13 then a morning test at 13 (13.5?) then it looks like you're winning.
Keep going another few days.