1. Sounds like you gave it everything you had, and that's all that can be asked of anyone. Sounds also like you've taken away some good from the experience, and that's more than most would do under the same circumstances, and that's also what'll put you in that group of finishers-of-rides-under-difficult-circumstances.
2. My take on PBP in '07 and '11 was that they simply were not enforcing the intermediary control times, period, at least for the 90-hour riders. I was in the 84-hour ride both times, and at a pace that put me at many of the controls when they were closed for anyone in the 90-hour group (yes, I know, and am accounting for, the fact that some 90 hour riders were 2-3 hours later than others due to their start times). Those controls were still open, and would be for a few more hours, for the 84-hour riders, so the volunteers were there anyway. I repeatedly saw riders trying to declare themselves out of time and being told "non, non!" get back on the road, you are ok, just make it to Paris in 90 hours and you will finish. A good friend of mine was an hour late to Villaines-la-Juehl in '11; he proceeded and finished in under 90 hours. Official, with pretty medal and all.
My unsolicited advice on the subject of "extra time" is, unless you hear it from the lips of the organizer himself, don't believe a word about "extra time" on a brevet. Ride as though all the control times apply, as written on your card. That said, unless a control worker takes your card from you and declares you out of time, keep riding.