I don't know if I'm reading your post correctly, but are you figuring your calories by day only? Your body will hold reserves over multiple days as necessary, so it might benefit you to figure your calorie intake over a week and use that. In other words, don't try to eat an extra 2000 calories on the cycling days and a regular level on the non-ride days. Split that amount into 1000 calories extra over the two days and it'll be a lot easier to get in the right calorie needs.

Last summer, when I was training for centuries, I'd ride for 6 hours on a Saturday and burn 2500 calories. That meant that I had 6 hours less in the day to make up those calories (besides the on-bike food which would never total 2500 calories). I just couldn't do it....especially when I was eating only healthy foods (it was too much volume of food). The only way I could hit the right totals was with crap food and that left me feeling like crap and then craving more crap on non-bike days. It was a viscious cycle. Anyway, my point is that if I had just eaten what was on my plan for the day accepting that I'd have a deficit for that day, and then make it up in the day following (or some on the day before), I would have been better off. Basically, I had to plan a week at a time. Of course, my goal was weight loss, but the concept is the same (just the amounts are different).