We will be spending 4 full days in Tokyo...
Our first full day we have booked a guide of the modern aspects of Tokyo..

Hoping to gets suggestions to organize our next 3 days.

We have 2 teen boys and I missed out on Studio Ghibli tickets. I still need to get the Robot Rest. tickets, but I'm trying to determine which night is best.

Spend a lot of time with japan-guide.com -- an excellent source of information.
http://www.japan-guide.com/e/e2164.html

http://www.timeout.com/tokyo

You didn't say when you are going but if it coincides with a Sumo Tournament or Baseball game, I think your teen boys would really enjoy either one (or both). You can easily buy tickets on line in advance. Both were great fun.

Where do I look for sumo dates??

Found this....
https://buysumotickets.com/sumo_event_calendar.html

When are you going? Sumo in Tokyo is in January, May and September only.

The baseball games are far different from US games - kind of a college football stadium atmosphere.

Here is the official Nihon Sumo Kyokai website:
http://www.sumo.or.jp/en/index

I suggest that you don't want the box seats.

I second the baseball suggestion - Meiji stadium (outdoor) as opposed to the Tokyo Dome (indoor). The crowd chants/songs/umbrella waving are incredible, as are the many eating opportunities and the 'beer girls'. In August, there is a fireworks display at the top of the seventh inning. As well as the Timeout site, take a look at Tokyo Cheapo website for ideas of outings/activities. There should be discounts available for the Robot Restaurant. You can still get to Studio Ghibli as part of a tour - I'm not sure what the price differential is though. Would help to know dates of your visit - Japanese culture is famously sensitive to the seasons- the calendar is marked by a cycle of festivals.