1. Can you select more than 5 ships at a time? If so, how? If not, why!? I need to go kill a pirate base.
You can, but you need to gain more logistics by researching some techs (in the engineering tree, I think).
If you want to increase the strength of your fleets, you can either research better weapons or defenses in order to make your ships more powerful, or research logistics and concentrate more ships in a fleet.
2. What exactly do 'minor' races do? Can you diplomatically get them to join your empire, or if you invade them, do they give you special ships/bonuses related to each particular minor race. Or are they just generic with a picture and occupy a planet?
They don't do much. You can exchange techs with them, curry their vote in the U.P., initiate trade routes with them, or invade them if you seek an extra planete.
3. How to invade a planet, what tech do I need to build troops?
You need the Planetary Invasion tech, (in the middle of the red tech tree, I think). It is in the yellow tech age, so you need to research about 15 techs before you can research it.
Once you have it, you can build Transport ships in your shipyard, and use them to invade.
4. What can you do about starbases from other players in your empire? I have some which I have totally surrounded with my influence, but as they got there first they seem to be taking all the resources, if there no peaceful way to turn it my side or get them to disband?
Not really, they won't flip to you. You can try to trade for them in the Diplomacy screen, but it will cost you much.
5.What does approval do? Does it effect your research/manufacturing or is it purely for resistance/influence/growth as it says (so not needed if I am already covered).
It also affects research and manufacturing, it is important to keep high approval when possible.
6. How does population affect the base research/manufacturing? I'm trying to work out if it is better to build farms or factories?
Not sure exactly, I know the formulas have been posted on the forum, but they should change with patch 1.02
Edit : Beaten by detailed answers to your questions.