I feel your pain. Earlier in the season, my little garden was infested with pepper maggots. It was awful - my best plants.
I researched all the available remedies, but concluded there was none. The flies deposit the eggs into the flesh of your pods earlier in the season, in what then looks like a whitened round-ish spot maybe 1 to 3 mm in radius. Those eggs then hatch on the inside of the pods and turn into maggots, which then eat the insides and eventually dig out through a hole. By the time you see the rot spot where the egg laying took place, or a hole where they crawled out, it is way, way, WAY too late. Like a month after the fact. The maggots are already inside the pods eating them. Which is somewhat unappetizing.
I think Sevin or other deterrent/extermination strategies must be implemented in the late June - early July timeframe to keep the flies from depositing the eggs in the first place. By the time they've done so, it is too late.
I threw out the affected pods, but it was only about 1/3 of some plants, and they eventually grew more pods. I am sorry to hear so many of yours are affected.
The most salient point may be that to add insult to injury, the maggots fall to the soil and burrow in and create nests from which next year's flies will emerge to deposit eggs. So basically, below your ruined plants is the next generation of maggots getting ready for the 2011 season. To whatever extent possible, the soil must be replaced or sterlized, or it's gonna be the same sorry drill next year.