How much rest (tendon or ligament), for a novice?
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.