I would play some stock first to get a feel for the game as is.
The big mods are:
Trigger Maru - reduces traffic to more realistic levels, includes a lot of graphical upgrades, makes enemy AI more difficult.
Reflections on the Water - Makes amazing upgrades to environmental detail, especially the water.
Natural Sinking Mechanics - Reworks the enemy ship damage model to make them sink in a much more realistic fashion, by flooding only.
Each of these will have to be updated post patch 1.4. Install order is still a little bit of a mystery to me, I installed Trigger Maru first, then ROW, and it seems to be working fine.
Also, make sure if you are running Vista you run JGSME elevated (i.e. right-click and select "Run as Administrator") or you may encounter problems with silent file redirection.
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