I think this winter will be time to completely re-evaluate my training and get all new baseline numbers. I just ordered up a Powertap hub and will be lacing it to a Kinlin hub to get some baseline FTP data. So as far as getting my threshold up, continue with the 3 minute intervals and add some 10 minute intervals to the mix? I'll probably work in burst power intermittently throughout the shorter intervals.
True, I am not as comfortable as I was holding a wheel and am not fighting to hold on nearly as much as I used to, but I am finding that I still feel fine with incidental contact etc.