How to recover a bad ride.

On bad backs, do not underestimate the long term strain put on the spine by carrying even small amounts of weight in a rucksack. I have long since given up using a rucksack (use a rack instead) and my back problems largely went away - if you don't believe me speak to a physio ! Curving the spine and putting weight on it is a terrible combination !
One thing you can do to help your back is use a foam roller (it can help restore the normal spinal curve).
On nutrition, a handful of brazil nuts really help - selenium is a handy mineral to top up on

Try a few iron tablets (or iron rich food)

I'm on a long commute at the moment too - 13 miles or so each way. To be honest I'm finding the sore back is the worst bit at the moment - even with the warm weather and hence pretty light backpack, it hurts.
As for fatigue - a glass of milk after each leg can help a bit. Eat well during the day too. But in the end, putting in long commutes either side of a long day at work is just tiring. Take a rest day when you can, I guess.

Rest - including sleep, as mentioned above - is vital to recovery.

If you can't skip a ride you really should make yourself spin an easy gear for a couple of days then stay off the bike over the weekend.

I know of people training who use a HRM as it's the only way to prevent their effort and heart rate going above a certain level (65 or 70% of max). You'd be surprised how hard it is keepig a lid on it!

You could try a proprietary recovery potion but they're expensive.

Assuming it is just the odd day and not a result of too much long term fatigue it can occasionally be down to not enough carbs if you have not been replenishig what you have been burning during rides. In honesty its more likely that you went a bit too much into the red a couple of days prior to your 'tired' day.
Also lack of sleep or stress can all take its toll, both in acute and chronic situations. If its just the odd day then 200mg of caffeine and a handfull of haribo will keep you going- not a long term solution though.

I commute 20 miles a day, 5 days a week and there is no doubt you plateau. The only way round this is to rest or vary your workload (eg target flat sprints or short hills on your commute) and try and ride easier on one day a week (think glass pedals to ease up on the power).
Not every day is a PB day !