Maybe move the saddle 1/2 way back to where it was? How much did you change it? The toe lifting does seem like it could be related o the height. Any other issues related to saddle height? It seems like if the saddle were too high, you'd have other issues over 77 miles.

My DH always has black nails from running - especially after trail runs with big downhills where his feet get shoved forward. I used to get them sometimes from ski boots, back when I used to stride.

Good luck. Fortunately, black toenails aren't a huge deal. Black TOES on the other hand, would be scary!