Help! I am so confused with the Robotech storyline?

I finally watched the original 85 episodes of Robotech and he Shadow Chronicles movie, but I am more confused than ever with it's twisted storyline. First off, Protoculture started out as technology from an alien race in the Macross Saga, then it became a catalyst for the mutation of the "Flower of Life" in The Masters/ Second Cross. Then protoculture becomes an energy source in New Generation?WTF?!!! Then there's the issue with the disappearing Zendreadi in "The Masters" saga. Somehow Dana is around, but there is no other Zendreadi? Then in New Generation, there is no mention of Dana, Zor, or Musica when supposedly they were the reason for the end of the second Robotech war. Then the ending of New Generation confused me because in Shadow Chronicles Scott and Aria are together, while in New Generation, he leaves her. Not to mention all the time differences between when Scott leaves Earth. Now I know that Robotech was three completely different animes fused together and given a large storyline for syndication purposes, but the storyline confuses the heck out of me. Is there anyone who understands these holes?