Nice job on a LOOONNNNG course. Wow.
It can be frustrating when you're in the swim following the people in front of you when suddenly you realize every single one of you was off course. That happened to me in Ironman Coeur d'Alene this year. It sucked. But what can you do. No mucho.
You know, I totally agree with you about how you talk about knowing the bike course. In my experience, it ALWAYS is better to know the course. It not only makes the mile fly by more quickly -- it really does when you know the course -- but it also prepares you for what's ahead.
Where you wondered if this was "a smart thing" for you to do because you felt your training was off, you may not have realized that you had one training aid in particular that can aid all other deficiencies in fitness, and that is the will to succeed. You obviously wanted this very badly, so bad to overcome all esle. And you did it.
Be proud.