If the timing was out by 3 teeth if probably wouldnt run or at least you would have a cam postion sensor fault as the cam and crank would be out of sync in the ecu.
Are you sure you have the cam pin in the correct slot.? Have you tried putting the crank tooling on first and then seeing if the cam pin goes in, there might be 2 slots in the cam and you are in the wrong one.
If you are sure your going to set it as per the tooling you have I would mark the cam and crank as they are now before altering it. And definatly make sure you turn it over twice by hand once its all set.
There should be marks on the belt which will also line up with marks on the pulleys, there are on the 1.9 so I would expect tem to be there on the 2.4, if they wont line up once you have set it in the new position then something is wrong.