Do you know what I am doing wrong here?
Yes, you've got an easy to fix issue, some of the files in the map are terrain data.
Here's what I usually do:
Everything named 'war3map.xxx' is a part of the map -- like triggers or unit data -- and you just want some of them. Namely:
- war3map.w3u is the unit data
- war3map.w3a is the ability data
- war3map.w3h is the buff data
- war3map.w3q is the upgrade data
The list goes on, you can check these file types by going into the World Editor's object editor and doing 'Export Unit Settings', and looking at the extension like .w3u on the end. There is a different file for each of the Object Editor data types.
The other thing you want is triggers. Those are in a special file, 'war3map.j', that is filled with JASS. This is the hardest part -- you cannot replace 'war3map.j' without messing up most melee maps. When I make mods, I usually open 'war3map.j' from my map and copy the triggers into 'Scripts\Blizzard.j' which you must extract from 'war3patch.mpq' and add specifically to your custom MPQ contents.
Basically, the MPQ Editor program makes a MPQ (think of it like a ZIP file) and then the MPQDraft makes a EXE (a program) that injects into Warcraft any custom data you put into this ZIP-like file. So if you put custom map unit data, and custom model files, it will inject them into the game for every map you play.