Hi,
On the glazing question, I would not use plexiglass at all, as it will probably not hold up to collector temperatures. This is especially true for the inner layer on a double glazed collector. For plastic glazing, polycarbonate is probably the best choice -- its good up to 270F. A rundown on different glazing materials here:
http://www.builditsolar.com/Projects/SpaceHeating/Glazing.htm
Using double glazing will cut the heat loss from the collector and improve its efficiency, but the 2nd layer also absorbs about 10% of the incoming solar energy, so its a tradeoff. If you live in a cold climate it will give you a more efficient collector. On the other hand if you use that 2nd piece of glazing to make a 2nd collector, that will double your output
On the length of the can runs, I'd say that from a best efficiency point of view you want the shortest can run that will heat the air to a useful temperature. Useful for space heating probably means at least 100F. The longer you make the can runs, the hotter the average inside temperature of the collector is, and the greater its losses out the glazing. But, the gain you get may just not be worth the extra complication that shorter runs would make for.
You might take a look at some of the links on can collectors and see what kind of temperature rise others are achieving with full length can runs -- if these are in the 50F or less area, I don't think you would get much benefit out of shorter runs.
Some links here:
http://www.builditsolar.com/Projects/SpaceHeating/Space_Heating.htm#Active
Down the page a bit -- search for "Beer".
Using more airflow also will keep the temperature rise for each can row down, and improve the efficiency and heat output for the collector, but bigger fans use more power, so there is a tradeoff there to.
This is a page on collector efficiencies you might find helpful:
http://www.builditsolar.com/References/Measurements/CollectorPerformance.htm
I'm a fan of the bigger is better rule for collectors.
Gary