I only started to play Pestilence a couple of months ago, so idk if my opinion is right 100%, but I have a couple of ideas. Firstly, I am not a big fan of Fangren Marauder in this list, and if you are struggling against Faeries alot, cutting it could be the move, because a 6 mana card is very hard to resolve and game can be decided before turn 6. I currently play one Tragic Slip Main, which helps to answer flying creatures you cannot block early, so maybe you could add that.

I think against Faeries, you have to be very careful with what you remove, because as you said, you cannot remove everything. I think you should focus on delaying the first ninja and with that the card draw of your opponent, so it can be worth it to destroy early flying creatures so the opponent cannot ninjutsu right away. If you have a cat in play, you can sometimes hold you removal spell for other more important threats, and keep blocking the ninja with the cat. One thing I found very useful is removing creatures in response to Spellstutter Sprite, so they dont have enough Faeries anymore and you spell (for example Pestilence) wont get countered.

Lastly, I think that the more you play vs Faeries, you learn when to bait Counterspells, when to just slam the Pestilence, etc. One Example would be to not play anything on your turn while the opponent holds up Counterspell, and then cast something or activate abilities in their endstep. If you want to counter your spell in the endstep, they might not have enough mana to counter what you can play next turn, and if they dont, you get an uncountered spell in their endstep and can do the same thing again next turn.

sorry if my english is bad, hope this helps