I would do as your first suggested, get rid of some of the stucco and get the bow out of the board and do the 3,4,5 method again and see how close you get. If the ledger board is straight you will get a more true reading on the squareness of the deck. If you can get it to 1/2" or less you will be alright. You can compensate the gaps between the boards to make up the difference over several boards.
I just built my mom a deck last weekend, did my own last year and am doing a 2 tiered deck at my new house in a month. I must be nuts.