The spot where the marks line up is where the mechanism ideally starts to lift the clutch.
To get more free play you turn the screw in...you know that, right? The other end of the cable might have come loose...you could check that.
I'm thinking it would work to remove only one fork cap. The other side would control it and just one spring would be easier to lean on and bottom out the coils. With a zip tie on the tube it would mark how far it went down or how far you could go before the fender hit something.
Still if you...
No, I was being a smart ass but I must be the one that missed something. I thought that as you take off the second fork cap that without pushing on the bars the weight of the bike would immediatly collapse the forks and shoot out springs and oil all over. And they would go down much farther than...
You said it was fine before...based on that you could try taking that piece off and examine to see if it all looks in place when you put it back on. Even if it is right, you must adjust the cable so it has proper slack or free play. The hand lever should pull the cable 2-3 mm before the cable...