What doesn't kill you makes you stronger

100 miles.
5 hours 26 minutes
6903 feet of ascent
8500 calories

Well, measuring 10 mile splits for evens plus a bit in hand was the plan. If I'd managed to stay on schedule I'd have come in at 4:55 and been happy with that. For the first 50 miles I was slightly up on schedule and although my back and knees were aching I was thinking all was looking good.
But.
At about 60 miles I had a visit from the man with the hammer. He didn't F*** off for the next 40 miles and by the time the century was up I was crawling around in the 42 ring battling an unbelievable headwind on the second, southern half of the course losing 30 minutes in 40 miles and not even able to stay on the tri bars and put any power down. Things are not looking good for the 12 hour and I'm worried that riding fixed all these years is doing my knees in. suggestions for exercises anyone?