Pixelmon Mod

Preferably without losing data. I'm playing with someone else and I'd like to put up a dedicated server so they can play without me around. The thing is, I seem to be missing some player data since it isn't as simple as just moving the world to the server.

Yes.
The player files are stored in the world and should transfer over just fine.
Are you missing your inventory or is someone else missing theirs?

Check the worldname/playerdata folder for the Players inventory files. they should be in the format of <uuid>.dat
you can use http://mcuuid.net/ to find out what file belongs to whom.