For control questions, check the file configs/default.ini (assuming you're using a joystick -- keyboard_only.ini if not), the key chart that should have come with the game, or read the fine manual. Briefly, though: 'T' or joy button 2 is target visually, 'Home' jumps to the top of the contact list (it's sorted by distance), and holding joy button 2 rolls instead of yawing.
Dodging missiles comes up all the time: it's quite hard to do in the tug, but not impossible. Divert all power to engines, combine multiple thrusters for more overall acceleration, and remember your Z laterals are far more powerful than your X and Y, so if you need to turn sharply left, you should face that way and thrust forward, rather than using X laterals. Double-tapping 'L' is a very effective way to confuse the targeting AI (it is almost a bug exploit, but never mind that). If all else fails, don't forget that LDSi detonations destroy any missiles in their blast radius.
Most mods that significantly alter gameplay should be avoided until you've finished the game and are just fooling around with it (whether in a second play-through or free-form mode) -- the unmodded game's scripted missions are sometimes flaky enough anyway without help from extra scripts with which they weren't written to work. Multimod is required by the majority of others. No launch sequence is a good sanity preserver. Custom Jafs is helpful if you feel the originally intended 12-pod capacity per haul is unreasonably limiting (combine it with the colossus for a 360-pod capacity, which I defy anyone to have the patience actually to fill). FutureTrader is good if you can't be bothered to find the items you need for desirable trades. iFleet is well worth playing, but I wouldn't try to combine it with the original missions -- it's essentially a mini-game in its own right. Unleashed, another mod you really don't want to go near outside free-form mode, does some interesting things you won't see anywhere else. The Elite mod is the most complete released rebalance mod I'm aware of; it may interest you if you become irritated with how overpowered player ships are.
