<p>I'm on a little quest of merging the structure of two MySql databases. Is there a tool for this with the might of Red-Gate's SQL Compare? Are there any free alternatives?</p>

although i dont have any experience with it, i hear that navicat would be the tool to use:
https://www.navicat.com/en/products/navicat-for-mysql
also toad for mysql i hear isnt bad:
http://www.quest.com/toad-for-mysql/