I am trying to get the lowdown on rigging and tuning our boat and have read the guides on the forums but still have a few beginners queries :)

Firstly to calibrate the rake of the mast and the various settings for this i am unsure of the best way to ensure that the boat is level along the bow-stern line. One suggestion given to me was a spirit level on the thwart, would this provide me with a reasonable starting point to begin calibrating the mast rake settings? i sail from a coastal club so getting an idea of when the boat is flat on the water is nigh on impossible.

Second, at present we generally set the rigging up before going out and leave the lowers snugged up tight. I have noticed however that when beating the leeward lower is under tension, whilst the windward lower becomes quite noticably slack. The general questions i have are is this how it should be, and what forces cause the mast to be bent to windward in the lower section?

I understand these are probably really simple questions and have stupidly easy answers but please bear with me, i'm new to all these bits of string!

I would suggest a spirit level vertically up and down the stem to find uprightness, the stem being at right angles to the waterline, generally speaking. As regards the bottom of the mast bowing to windward, is this caused by the tip falling off to leewards as the rig powers up? Generally, you allow some prebend in the mast (say about 2 ins at spreader height) before tightening the lowers, such prebend being induced by rakeing the spreaders aft. 
No doubt others will chip in with their views.

Try the transom as the vrtical datum. As far I am aware the stem does not actually have to be vertical, it may be on more modern boats, but I am sure I've seen a few older ones that angled aft slighty.

A tight kicker will push the mast away from the boom. If you have the boom over the rear quarter (rather than down the middle of the boat), then the lower part of the mast will be pushed to windward as well as forward: thus the leeward lower could easily become very tight.
One of the purposes of the lowers is to help keep the gooseneck where it is supposed to be: i.e. you put them on to counteract the push of the kicker.