Which jr pass and when to activate

Greetings, firstly thankyou for such a helpful site!
Not sure whether to get 1,2 or 3 week pass and when to activate?
Itinerary ( accom booked already ) is as follows
arrive18sep narita express, staying harijuku * in tokyo 4 nights seeing sights and a day trip to kamakura * 22 sep shinkansen to Nagano then on to matsumoto, stay night(last train trip til 28th sep, hiring car 23 sep dropping in kanazawa) 28 th sep train from kanazawa to kyoto 28 sep- 1 st October local travel around kyoto 2nd oct train to koyo San 3rd oct train to osaka , trips from osaka to himeji and Nara til 6 th oct 7 th October shinkansen to tokyo *8 th narita express

Your help would be soooooo appreciated. In hindsight I should have hired car at end of trip, but all is booked now. Thanking you in advance!