I think you are confusing those trying to help you. Did you post an old screenshot? Is your .MODS tab still missing?
Giving permission to groups (Administrators, Global Moderator, Registered Members, Newly Registered Members, etc).
Because when the author said for you to set permission, he meant for you to click the Permissions tab, Under Global permissions - click Groups' permissions, select a group in the drop-down box and click Submit, Then click Advanced Permissions and you should see a Reputation
tab. That's where you decide each groups permission for the reputation mod
Note: You have to do the above steps for each group you have in your dropdown in your forum.
Setting Forums Permissions
Then you also have to set forums permission for all the forums you have on your board. That's where you can leave out forums you don't want reputation to show
Permissions Tab, under Forum based permissions - click Forum permissions, highlight the forums or click the checkbox All Forums and hit Submit, Under Groups - highlight to do individually or check Select all Groups and click Edit permissions, click Advanced Permissions next to each forums one by one and you should see a Reputation
tab. There you can decide if that particular forum should have reputation showing and you if you want users to give negative rep in that forum.