You're going the right way on the mods. First play the game stock at version 1.3 to get a feel for the defaults. It will also help you learn manual targeting to have all the helps on the attack screen. When you're ready, the mod du jour and standard of the industry is Trigger Maru 1.6 by Ducimus, who you should already know from SH3. Then there are a few mods you can stack on top of TM, but as usual, with care that you don't make unplanned changes in the underlying supermod.
Oh.....strategy tip. Don't forget all you learned in SH3. Although the American method of planning an attack and working the TDC is entirely different from U-Boat strategy, all those U-Boat strategies do not care what nationality submarine they are used in! We have discovered that Dick O'Kane did just that, using the TDC in the same manner as the Germans did and not using our fancy Position Keeper at all. By all means learn the new toys, but never forget what you learned in the Atlantic. Use it and prosper from having more tricks in your ditty bag than the average bear.