Spacing between solar arrays

If you're in the northern hemisphere, the lower angle of the sun in the winter is probably contributing to your low numbers. (When the sun is low in the sky it passes through more atmosphere to reach the ground.) Presumably you'll do better in the summer.

Also, the tilt angle of the panels should be matched to your latitude. If your panels are mounted on your roof and aren't at the optimum angle (or aren't pointed directly south), that would decrease your efficiency. In any event, unless you have tracking panels or constantly change the tilt, your panels will only be pointed exactly at the sun twice a year, and at all other times will be slightly misaligned.

This website has a detailed description of tilt angles, but the net result is that if you have a fixed array at the optimum angle, you'll only be getting 71% of the exposure than if you had a tracking array constantly pointed at the sun. If your angle is not optimum you will do even worse, obviously.

EDIT: I should also point out that your definition of "optimum angle" for a fixed array is dependent on what you're trying to optimize. There are a couple of ways to look at it:

1. Generate as much power as possible over the entire year. The 71% refers to this option.
2. Generate as much power as possible in the summer, when electricity usage may be higher due to AC and/or power may cost more to buy from the grid. This will be a lower angle [array pointed more upwards] than 1), since the sun is higher in the sky in the summer. Winter usage will be lower than 1).
3. Try to generate power evenly throughout the year. This will be a larger angle [array pointed more towards the horizon]. This approach tries to increase power generation in the winter relative to 1), at the expense of some summer power.

Having the coil connections crossed over will decrease the efficiency of system. In the worst case it would be better to turn off the solar part of the system than have it run as installed!

In a heat exchanger like this, you want the outgoing fluid to be as cold as possible. For this reason you want it exiting the bottom of the tank where the water is colder.

In your case it might be so bad that hot water tank is heating the fluid above the input temperature and that the solar system is actually removing heat from the hot water tank. Even if it's not that bad it's definitely not good.

For more information look into counter-flow heat exchangers.

I don't know what would cause the pressure drop but I would agree with you that it appears your air separate was not installed as per the manual.