AFAIK you can stop spies, by exposing them. It cost money though. 1.27F did fix a few things, but not much. It is always a good idea to patch up.
AFAIK the lost always works that way, unless you are at Chief, thenit does nothing.
4 turn is the lowest, but you can change that in your BIQ and I would expect in BIX (PTW). The dialing down is only effective, if you put in more beakers than the cost. This will usualy be the case, but not always. The amount "saved" varies and may be quite small.
If it is quite large, you should have turned down the science at the start. It is like income tax withholding. Some like to let them take a bit extra to get a refund, others think it is better to have the money all along.
Tech pace is a function of several things, map size, tech cost and so on. It should not be possible to get to 4 techs right out of the gate and stay there. Later you can get efficeint enough to do it.
You could raise the cost in the BIX.
Improvements were make in C3C, not sure how well it functions though. Mostly it revolves around the ability to get a game going and keep it form crashing.