New Year Travel Advice

Hello,

My husband and I will be flying into Tokyo via Narita on the 30th of December and plan to activate the 7 day pass by using it on the N'EX train. We also plan to take a trip to Kyoto and Osaka on Jan 2 and 3 with a return to Tokyo on the afternoon of December 3. Our plan is:

Dec. 30 - Narita - Tokyo N'EX
Jan. 2 early morning - Tokyo - Kyoto, sleep in Kyoto
Jan. 3 morning - Kyoto - Osaka full day
Jan. 3 afternoon around 4 or 5 - Osaka to Kyoto
Jan. 5 Tokyo - Narita on N'EX

My question is, is Dec. 30 a little late for us to be making seat reservations for the Tokyo-Kyoto, Kyoto-Osaka and then Osaka-Tokyo trips? We arrive around 7pm at the Shinjuku station and I'm not sure the JR Office by the South Gate will be closed by that time. Will our chance of getting seats be higher if we got a green pass instead of the regular? Also, if we have a green pass, is it okay to just hop onto any unreserved car? I appreciate all your input, thank you!