It sounds like you're running into the same project as me. I have all 4402's and was considering upgrading to a 5508 for our headquarters. This happens to be our guest anchor as well. To ensure that mobility will work, which is a requirement for guest, carefully read the version 6 release notes. In a nutshell though, I've found that this will work with 4.2 code and up to version 6 on a 5508. I'd check the release notes to be exactly sure of the 4.2 release though. 4.2.205.0 has been working well for me. I don't have our 5508 yet, but I'll provide an update once it gets here. In a perfect world, having the same version 6 release on the 4402's and the 5508 will ensure you don't have anchor / mobility problems.

As far as the different AP licenses go on the controllers, this will only affect the size of the network you can have at each site (because it restricts the number of AP's, ie. 25 versus 12). You can definitely use guest on a 50 AP controller with a 12AP controller at the other site. They don't have to match...