To be honest Andy, I think I had the opposite problem, and didn't train enough.
But first, I'd better clarify that the injury was in the Chicago marathon, not the London. For the Chicago race, my training was patchy. I missed several long runs, and in the later part of the training, I don't think I completed a single week as the schedule said I should.
I might be wrong, but I felt that the bad knee I got during the race was because I hadn't done enough mileage.
For the London race, 6 months earlier, I followed the programme more rigorously - though even then I missed several runs.
For your own training, I'd be slightly anxious about you missing what Hal calls the "kinda long" runs on Wednesdays. Even if you can't do the full length, a short jog would be better than nothing. I wonder if you're overdoing the weekend long runs? The important thing to remember is that although these are long, they are supposed to be SLOW. To be honest, you should leave your watch at home and just concentrate on getting to the distance (not that I managed to do that...)
I seem to recall Hal saying that the weekend long runs should be a minute or two slower than race pace.
Another thing you might try is a good sports massage on the Monday, or even a swim, to help you recover. But as always, the old cliche about listening to your body is the best advice, and as the coach says, undertraining is better than overtraining.
Are you managing to do all the long runs so far? I guess you'll have done 18 miles by now?
But in answer to your question, I have to say that I was probably too lenient with myself. But the reason that I missed so many runs wasn't that my body was telling me to stop, but just that I was working very long hours and couldn't fit them all in. If your body is saying that you can't do the long Wednesday run, then fair enough. Don't do it.
Is this your first marathon by the way?
Finally, remember that you can ask Hal himself for advice on his training programmes. Plenty of other people do. Got to
http://www.doitsports.com/vt/index.tcl and sign up.
Keep us posted.
Andy