I would do the board and batten all across the top floor in a co-ordinating color or match the stucco which IMO will be hard to do and not look like you tried and missed.Put the window boxes on the bottom and remove the bush that hides the window , in fact landscaping will be the next item to fix.. I would also redo the portico with something a bit simpler in style that suits the house, add a walkway from the street to the front door too

Does the tarp cover a large window? Is the wall of the addition set back? Is that why the roofs don't align? The existing eave doesn't look straight. Take a photo showing the corner.

Thanks, there will ultimately be 2 windows where the tarp is (aligned with the 2 windows below). The wall of the addition is not setback (even with current house), but the roof line is a touch lower. I will try to update photo tomorrow. Thank you!

If you're not going to do siding across the entire second floor (as suggested by Patricia) then I would just match the stucco. Otherwise it's going to look like an addition, instead of just part of the house. You could do another siding style if you don't want to the the B & B.

If you're interested in seeing how stucco or siding would look check out my web site, Creative Visual Concepts. I could show you how these different treatments could look on your home.