A way to make a server side mod with Bukkit?

I have been trying to integrate a few mods with server side support from the Minecraft Forums into Bukkit, but they are all build for the original minecraft_server.jar, and thus, the code is obfuscated. However, when I deobfuscate the code, and try to paste it into the Bukkit jar, the files don't match up. This is especially true with the NetworkManager.java file, which never seems to work. Is there something in Bukkit that prevents the loading of anything non-stock from the stock Minecraft server? I especially want to port SDK's GunMod so I can use iConomy and let people buy guns. Thanks.

 

The gun mod would be very difficult, it would require all of your players to have a clientside mod, etc.

 

Pogic is trying to implement this, and apparently it does require Bukkit modifications to work, meaning it will probably break plugins...
And yes, I don't mind having everyone install the client mod, that's fine by me.