Oh the joy of learning to sail

1. In choppy water, the board was very difficult to turn (not sure because of too big board or whether my sail has a lower CE). Even tacking took effort.
A big board in those conditions will be a handful. Not much to suggest except that one day you'll love those conditions. I can only suggest more practice to get used to it.
2. Going very board reach without the harness lines was difficult (I wanted to go home). If I stood too far behind, the board sunk. if I didn't stand too far behind, the strong wind pulled the sail and my arms hurt.
Not trying to be funny but that is what the harness is for!! When you get comfortable in a harness, there will be no strain on your arms and you can sail that way for hours. With the harness lines taking your weight, you won't have the problem of the tail sinking, your weight is transferred to the mast base which is in the centre of the board. If the board is not planning, all the force is just dragging the board through the water, and that takes a lot of effort. Because planning takes less force, the force on your arms will be less as well. If you can get the board planning, it will be less strain on you arms even if you aren't using the harness.
3. non-planing carve gybe was difficult, stepping on the leeward rail did not turn the board that much. The choppy water made me very difficult to keep balance.
When you aren't planning, the way to turn the board is with the sail, not by sinking a rail. Have a look at some footage of a slow gybe and how you position the sail. In the future you will be carving around, that is when you can bank the board and use that to turn. It's great fun though a carve gybe is a goal that requires a bit of work to perfect.
4. Planing: Still not into footstrap yet. Once I sit down on my seat harness with my ankle almost 90 degree, the board speed increased. The choppy water made the board very hard to balance. My front foot was stepping on the front foot strap for a short while. The unstable board just made me not confident of putting into straps yet. What should I do? I am not in a position to buy smaller board because I don't think my skills are good enough for a smaller board
Keep your back foot toward the centre line of the board, you don't want to bank the board over otherwise you will carve up into the wind and lose speed. Your weight will be mainly on the back foot, this will mean that you can move your front foot and not upset the trim of the board. You say that your front foot is stepping on the footstrap, just slip it in, this will give you better control of the board and should make your riding easier not harder. If you have adjustable straps, put them into inner positions as well, this will make it easier to get used to them.