Thomas - I feel your pain having failed to do sub 3 the first time by 49 secs myself.
You say that you "didn't feel any discomfort until a few hours post run" - wasn't the cramp you suffered discomfort? Can't believe you ran in different shoes than what you had trained in. This is almost certainly the cause of your cramp and I am really surprised that none of your advisors warned against this. When you are pushing hard to achieve a goal it can be all down to the detail. I have always worn the same make/model of shoe. I buy a new pair for London but make sure that I have broken them in for a 100 miles by the day of the race.
My best advice for next time is change nothing from your long training runs and I am sure you will do it.
Golfer - to achieve my sub 3 I pretty much followed the Runners World free sub 3 schedule which peaks at 60+ miles/week during March.
I tend to concentrate on average pace for the week which would be a lot higher than normally recommended.
The last time I did sub 3 a typical week looked like this.
61.33 MILES @ 7:12 with 6,822 ft ascent and 6,762 descent. This is taken directly off my Garmin for March 2012.
Thomas - as Steve says no need to aggravate your niggle with speed work or track or hills. If you don't do any of these between now and the race you will still easily achieve sub3. Do those sessions unneccesarily and it may stop you making the start line.You cannot improve your performance during the taper but you can ruin it!