You will need a save after the second side mission and before the Krillen battle to do Side 3a&b. All you will need to do is travel to Beehive Station to initiate. Note that it needs to be at least 5 days after the 2nd side mission was completed. There is a significant amount of content in this side mission (couple hundred images). The other two little items are very short sequences and not worth investing much time in order to trigger.Just finished the game but according to the Quest Tracker I missed a few things:
-Trading Lessons G
-Side Mission 3a
-Side Mission 3b
-Shower A
They are all in Red listed as Bypassed. Not sure how I missed them or if there is any way to view them without playing all over again.