Your calf pain can be mild grade chronic exertional compartment syndrome
(CECS).The other possibility can be calf muscle injury. Since there are only some fibers of the muscle, which are injured; most of the activities are not hampered and pain only comes only on specific work (when these fibers come in to the play).
The pain above the left knee and hamstring can be due to following;
1) Tight hamstrings.
2) Strain of these muscles; which is secondary due to calf issue (abnormal stress on these muscles due to shifting of line of weight bearing).
The treatment entails;
1) Stopping running for two weeks.
2) Stretching and strengthening exercises in the supervision of a physical therapist or an MD in physical medicine and rehabilitation.
3) Swimming after two weeks.
4) Exercises in the pool.
5) Deep electrotherapy; iontophoresis / phonophoresis / short wave diathermy.
The running is resumed after 4-5 weeks; very gradually increasing the distance.
Please feel free for your follow up questions.
I would be happy to assist you further, if you need any more information.