1. What is the advantage of using a Power Mosfet at the input over going instead directly in with the DC?
That transistor is for input reverse polarity protection. If you apply 12V backwards, the FET will stay off and block the current.
2. According to the JCK datasheet it can accept a max current in of 2.8A, would a 2.5A fuse (Fuse1) be ok/safe?
Well, it is hard to say. I would guess that the fuse might not blow very fast at 3 A. But the connector probably won't heat up very fast at only a slight over-current. So it may be OK. Maybe a 2 A fuse would be more prudent.
3. Will there be an in-rush current to consider when selecting the proper fuse? Also for fuse 2 and 3?
Inrush probably won't be a problem for fuse 1 because the big cap is in front of the fuse. Inrush does not go through the fuse. For fuses 2 and 3 it depends on what is attached to CN1. If the load shows high inrush, then maybe it could be a problem.
4. Do the outputs of the JCK need to be regulated?
Honestly I don't really understand the question. The jack goes straight to a regulator already. I don't think it makes sense to put another regulator between the jack and the existing regulator.