Use no more than two 90° elbows (one above the stove and one on exterior), just make sure that the horizontal section of the pipe will rise at least ¼” per foot with the highest point being at the thimble / wall penetration.
Chimney clearance to wall finishes will depend on the type of the chimney you’re going to purchase and on the wall finish itself. For non-combustible finishes i.e., stone, brick, and cinder block that clearance requirement will be most likely “0”. For any combustible materials stove chimney clearance might be 2” like for this DuraTech stainless steel chimney system -http://www.duravent.com/Product.aspx?hProduct=2
or some different value
As for the window I’m not aware of any laws preventing it from being installed behind the stove. It might become an issue if this is the only window in that area of your home that can be used for emergency (fire, etc.) egress (for a fireman) or exit for the occupants. Depending on its exact location it may also look awkward to have a chimney installed in front of a window…
I can’t see any drawings after clicking at your link, just a set of drawing tools.
Let me know if you have more questions, just click “comment” below.