So I've been having a blast with the mod with a friend of mine, however on my side the ammo indicators are slightly moved to the left.

It is by no means unplayable, it's just annoying. This only happens on co-op, I've tried to uninstall everything but no dice.

Perhaps anyone can point me out to a solution? :)

Here's an image of the issue: http://imgur.com/Uo60lhv

That is a known issue (a regression after making HUD draw in pause menu correctly) and will be fixed in the next release. The only "fix" would be to write/use a mod that draws custom HUD (e.g. there's HUDit).

Depending on what you are playing the mod for and how much you are concerned, reverting to 9883 would work for avoiding the issue.