Some places I like to visit when crossing the state:
Colonial Photo and Hobby in Orlando http://www.colonialphotohobby.com : Just an awesome old-school hobby shop. It's about a third model trains, a third photo gear (lots of good stuff in stock) and then a third "misc. hobbies:" r/c cars, slot cars, rockets, plastic models, etc.
Skycraft Surplus in Orlando http://www.skycraftsurplus.com : If you ever wanted to build a battle-bot or UFO, this is the place. You can buy O-rings, nozzles or diamond plate by the load. Just cool. Plus it's right off I-4 so it's not too far out of the way.
Downtown Winter Park is just a neat place to walk around. It's the same exit as Skycraft. The Morse Museum, located in Winter Park, has a huuuuge Tiffany glass collection: http://www.morsemuseum.org
Even though it's right off the highway, getting there is a pain: http://www.ferraricf.com .
When are you passing through Daytona? Don't forget that the Rolex 24 At Daytona takes place during the end of January and we're doing our big party: http://grassrootsmotorsports.com/events/daytona-experience/
Rolex test days take place Jan. 4-6.
If you're coming through Daytona, there's The Race Place--our official slot car supply house. It's on Cave Avenue in Holly Hill, right around the corner from our new building.
While at Merritt Island you have to see the Manatees: http://www.fws.gov/Merrittisland/Wildlife.html . We were actually there last week. For whatever reason, there's a spot where manatees like to hang out. We saw four or five there last weekend.
Orlando Wetland Park is also neat: http://www.nbbd.com/godo/orlandowetlands/
And I assume you're going to the Space Center, right?
As far as a place to stay between Orlando and Merritt Island, there's not much between the two unless you're coming up to Daytona. We just did that drive last week, too.