I'm not sure if I understand the first question right, but it sounds like your machine will have to tilt back further in the altitude direction to compensate for the fact that your machine probably isn't able to move far enough along the azimuth to point at the sun during certain months. Is that the right idea?
"Out of the box", the program won't calculate altitude angles past 90 degrees from the horizon, but I don't think that it would be very difficult to change that if needed. It would be a good problem to address because I can see how that would be a problem for people closer to the equator. Do you know what the physical movement restrictions are for your machine? It might be possible to have the program automatically figure out the best way to orient the machine based on those values.
For the best Arduino question, the quick answer is that either the Arduino Uno or the Arduino Mega 2560 would be best. Or at least, those are the two that I have tested.
The in depth info for this question is at this link. http://www.cerebralmeltdown.com/sun-harvester-shield-documentation/
I didn't realize that I was so low on limit switches. I'll have to order more. For a machine as large as yours though, you may consider using something more robust anyway. The ones that I've been selling are mainly for smallish machines.
If I can find a couple of extra limits around, I'll throw them in the package.
Thanks for the order!