Figured out what the Horn Shell and Whale Whisker is for (spoiler) Away: Shuffle Dungeon
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Equip the Horn Shell before doing the DNA dungeon. When you exit the dungeon, be sure to check out the shiny spot on the ground in front of the spaceship's control panel BEFORE talking to Professor Atom. An alien named Mepple will appear, make fun of you and then trade you the Horn Shell for the Zero-G Armor (that will go nicely with your Zero-G Axe).
Equip the Whale Whisker immediately after that. When you fly your spaceship into the future another shiny spot will appear in the same exact spot, right after you talk to Professor Tatom. The immortal Mepple will reappear, make fun of you again and then trade you the Whale Whisker for the Secret Scroll, which provides 100 extra EXP points.
Oh, and I don't think you get anything extra for completing the Flower Seed, Chisel and Paint side quests 100%. At least not that I could tell. I don't even know why they are there, other than to decorate your virtual world.