Alleged, I have to just repeat. I'd play the game stock or just Game Fixes Only Supermod at first. Don't worry about manual targeting. Don't worry about unlimited fuel/unlimited battery, turn 'em both on. What you need is enough playing time to get the basic game controls automatic, some basic approach and evasion stategy working and some shooting torpedoes without worrying too much if they're set right.
If you're not having fun ratchet back the difficulty until you're comfortable. Then add difficulty as you can handle it without terminal frustration.
The fun meter is your guide. If you're not having fun change something.