The first thing I noticed that could be the problem, is the first two lines of your post. Sounds like you need rest to me. Riding 5 to 6 times a week, you cannot do the same intensity on all days and expect your body to hold together. My suggestion would be to take 5 days off the bike, and let your body recover. Do easy rides the first two days back, and then continue on sort of like normal. But in the future, never do more than 2 days of hard intervals back to back (and switch up anaerobic and aerobic intervals when you do back to back), and give yourself active recovery days. You can do the 1-2hr rides during the week still, but if you do 2 or 3 days of intervals, just make a day a or two super easy spin around town enjoying the scenary.
You seem to be eating/drinking plenty, maybe even a bit much. My guess is more on the training and the overtraining, than the actual nutrition on the ride that day that is affecting you.