Get to Tokyo somehow (Narita express? - I don't need the JR pass for this?)
Stay in Tokyo area until 4/1;
Activate JR Pass on 4/1 (departing Japan 4/7);
Go to Kobe/Kyoto/Osaka ....... Staying with friends;
Return to Tokyo 4/6 & depart 4/7.
I see a JR Pass - special 3 day eastern Japan pass. - u cannot use it until April 1st and its good until June. However, this means I MUST activate the original pass for 3/29-30-31 and I cannot stay in Kobe area past 4/4; must return to activate the shorter pass.
A solution is if I can get to Tokyo and maneuver around the city for those first 3 days WITHOUT the JR pass. Can I get around easily on a different line and/or the subway??????????
It was a bit hard to understand your replay, so I hope my answer covers your question.
To get to Tokyo:
The most convenient way is the Narita Express, that leaves the Airport every 30 minutes and will bring you to the heart of Tokyo in style and comfort, it is covered by the JR-Pass but you can also buy a ticket for it, note that this train requires a reservation. Alternatively you can take a local train, which usually involves a transfer or two and starts at around 1,200Yen.
I think this is the special pass you were referring to, it however does not cover the Shinkansen to Osaka so I don't think it will be very use full for you.
If you stay in Tokyo a couple of days you won't need a JR-Pass, local travel is not very expansive and the Tokyo Subway will get you to most places. The Tokyo 1-day Metro Pass may be of use when you are there!