The Sunbow Marvel Archive is a fantastic fan run site "Dedicated to the preservation and showcase of scripts, storyboards and other production material from Sunbow Productions, Marvel Productions and their co-production partners.". They recently added a ton of material to their page in "Volume 5" and "Volume 6" updates. Here's the list of what they've added:
Volume 5
MP#700-36 Desertion of the Dinobots – Part One
MP#700-37 Desertion of the Dinobots – Part Two
MP#700-38 Blaster Blues
MP#700-39 A Decepticon Raider in King Arthur’s Court
MP#700-40 The Golden Lagoon
MP#700-41 The God Gambit (Previously available at the Archive via other sources, included for completeness)
MP#700-42 Make Tracks
MP#700-43 Child’s Play
MP#700-44 Quest for Survival
MP#700-45 The Secret of Omega Supreme
Volume 6
MP#700-46 The Gambler
MP#700-47 Kremzeek!
MP#700-48 Sea Change
MP#700-49 Triple Takeover
MP#700-50 Prime Target (formerly: Welcome to My Parlor)
MP#700-51 Auto-Bop
MP#700-52 The Search for Alpha Trion
MP#700-53 The Girl Who Loved Powerglide
MP#700-54 Hoist Goes Hollywood