CA,
I have had black toenails on both big toes simultaneously from running shoes with too short/small a toebox, but never from cycling shoes, even my Sidis (which I have since sold), which were about 1/2 a size too small for me. I've heard of people getting black toenail from running, hiking, and tennis, but not from cycling. Very curious! I will warn you, it takes FOREVER for the blasted things to get back to normal. I'm over a year out from mine, and they still aren't what I'd call 100% normal. They aren't black but are more ridgy and uneven than before. I was lucky that neither of my toenails fell off, but be prepared that that can happen too. Google "black toenail" for more information than you every dreamed possible!
Congrats on doing the MS 150! 
Emily
Emily
2011 Jamis Dakar XC "Toto" - Selle Italia Ldy Gel Flow
2007 Trek Pilot 5.0 WSD "Gloria" - Selle Italia Diva Gel Flow
2004 Bike Friday Petite Pocket Crusoe - Selle Italia Diva Gel Flow