I'm in Japan for 4/5weeks. I'm going to base myself out of Tokyo for 2 and half weeks and then base myself out of Kyoto for 2 weeks and try to go to Okinawa for 5 days.
1) Should I get a JR Pass (maximum pass is for 21 days)?
2) If I get the pass should I start using it when I leave Tokyo so I use majority of the pass on longer travels (from Kyoto I'm going to do day trips to other cities)?
It's not widely known, but there is regional train passes as well, so you might want to have a look at these too.
Tokyo and North regions
Kansai & Kyoto area
P.S. Okinawa doesn't have a train system like the rest of Japan, so I wouldn't have a pass during the days you are going to be there.
Hope this helps.
If you are going to Tokyo first, keep your JR pass and activate in on the inter-city haul, and make sure you only activate it from the first day you intend to use it. (if you don't activate it till e.g. 5pm that is then one day gone, even though it's not a full day) Around Tokyo, get yourself a suica card-covers all JR lines in the city and can also use it in other cities like Osaka and Kyoto on their local JR lines. Can buy it at airport, railway station, convenience stores. There is a card deposit charge-any credit you have left will be refunded if you take it to the specific counter at railways.
If you are going to Kyota/Osaka first, the ICOCA card works the same way as the suica. Look on the website and see if either will suit you. I have always found that it it is better to use the local card and keep your JR pass for the long trips. (JR pass will cover you for the ferry to Miyajima by the way.)