If the marks don't line up, your timing is off, and that will cause your rough running/no start problem. The chain may have been worn out, and got loose, making it possible to jump a few teeth..
I would recommend replacing the timing chain, and setting the timing back, to see how the car runs afterwards.
Place the timing chain on the sprockets in the right order, then slide the entire assembly on to the crank... it's a doable job by yourself, unless something was damaged, but as TDF stated these are non-interferance engines, so that shoud be minimal chance (if any)
A good haynes manual for that car would work wonders.. look up timing chain replacement.. hell maybe someone on here would type it up really quick.. (I don't have my haynes manual within the city or I wold be more than happy to do it, myself..
Ray