I tried reinstalling medmod on a new installation of Medieval just last week and also got a mess.
The secret is that you have to install it in the Total War folder - NOT the Medieval folder itself.
The Total War folder should be the folder one level above the Medieval Folder, ie your directory should look something like C:\program files\total war\medieval - total war\
I suggest uninstalling and reinstalling Medieval, then installing Medmod in the Total War folder.
Also, which version of the medmod you use depends on which version of Medieval you are running. Are you running MTW/VI, MTW 1.1, or MTW 1.0?
If you are running v1.0 you will have to patch it to 1.1 first. If you are running v1.1 then download and install the version of medmod that works with 1.1. Likewise if you're running MTW/VI then ensure you have patched it to v2.01 first, then download and install the medmod version for 2.01.
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