I think we resolved this as I remember seeing you in game, but I didn't want to leave this post un-replied just in case anyone else had this issue or anything. There was an issue with the sign due to one of the plugin updates, but it has been fixed now.
There are also two distinct types of mods, client and server.. If you are interested in making server mods, head on over to bukkit.org. As for client mods, im not too savvy with those, so I can't really give a good place to look for that.
Worldpainter is a good starting point for getting the general layout of your world. After that, the Voxel Sniper plugin is great for making custom details such as mountains an canyons.
Maybe check to see where the texture pack shortcut button takes you(in the texture pack menu)? If your minecraft is being stored elsewhere, it might take you to the right location.
There are some settings such as memory allocation and build version in the launcher that you might have some luck with. Also may be worth checking to see if java is the correct version.
