How much rest (tendon or ligament), for a novice? Given that 'training' is a valid topic, can you say how much rest a novice needs?

My ambition is to commute 18 km each way, every week day: in Toronto (mostly flat, some hills, mostly bike lanes and some bike paths). I have a bike and I am currently doing the 18 km in about an hour and a quarter (so, about two and a half hours total per weekday).

My schedule has been:


Full days (18 km each way, 40 km total) since the Tuesday before last (8 days ago)
No riding (complete rest) last weekend (2 days)
About 10 km/day, for the 6 days before that
Virtually no exercise (occasional 1 hour on an exercise cycle) before that (this is a new job and a new bike) ... so, I'm a novice
I'm 49 years old, have a sedentary (computer) job/life-style, male, not over-weight (6 foot / 185 cm and 170 lb / 77 kg).
It's been a little cold (down to about -8C; I've been wearing jeans, and caring more/only about my core temperature, so maybe the back of my knee got cold; certainly my feet got cold sometimes; it wasn't especially cold today though, about +4C, when the pain started)


I've been loving the rides, and I want to continue.

Today I developed a pain at the back of my knee at the top of my left fibula. I don't know whether that's a ligament or a tendon (I'm presuming it's one or the other). I'm using Shimano SPD shoes with the clip at the default position (centre of the ball of the foot). My right knee is fine. The one other thing I do with my left knee is, when I stop, I put my left foot down on the road: which means pointing my left foot down, putting my weight on my left toes (not heel), while my right foot is still on the right pedal; but maybe that's not relevent.

Towards the end of my ride I tried unclipping my left shoe, and rode with the pedal under my arch (instead of under the ball of my foot, to reduce the work being done by my calf ... because I couldn't work out why it's the back of my knee that's hurting: I would have expected the front, if most of the force/work is from the front thigh) and that seemed to help: less acute pain.

I don't care much about short-term pain, except that it might be a warning of worse chronic pain to follow.

Why am I getting that pain there? What should I do or change, to remedy it? Am I resting enough and if not how much more rest should I take?
I am not a doctor, so please take this with a grain of salt. 

You can't expect to go from zero training to big training in a week. You may try taking it slow, like two days a week at first, or three. Once you don't have a problem with that, go on for more. A 40km commute is nothing to be scoffed at. 

Personally, I avoid commuting below -2°C because if I don't wear special protective clothing, I get pain in the knees. I don't want to change clothing at work, therefore I take the bus when it is cold. 

Generally, knee pain can have a lot of sources: 


Lack of training - muscles in the knee not up to the job. Or lack of strength in the back, arms, shoulders leading to a sagging posture, off to one side, etc. 
Temperature
Pre-existing damage to your knee, that you didnt notice before (sedentary lifestyle)
Bicycle settings: seat height, handlebar width, distance, clip position etc. Experiment with it. 
Habits: different pattern of force application on the left leg. Always using it to start? Watch what you're doing. Move about the bike. Change the settings. 
Jeans might be interfering with the blood supply - try with bicycle pants. If you feel uncomfortable on the bike, this may be the reason. 
Saddle
etc.


My experience when I had a severely damaged shoulder, it became nearly impossible for me to bicycle, because I got problems in the left knee. I had ridden 10k km per year before. Left arm broken, left knee hurts. (Or any other improbable combination, really)

I then moved to a recumbent, and my right knee hurt when I did a 150km a week commute. After much experiment, I noticed the pain stops when I move a few centimeters to the right of the seat. 

After the accident and before getting the recumbent, I slouched for three years, with next to no bicycling. When getting back on the bike, despite having ridden so much before, it took an astoundingly long time to get back to the 150km commute (44yo, sedentary lifestyle)

After some training on the recumbent, there is no problem on the upright any more. Okay, the shoulder is 95% fine now. This took two years, though.