Vinyl not so bad to work with when you get used to it. It's kinda like a ziplock bag.
I would only remove the siding where the deck is going to be, not the whole 5'. All you would need to do this is some J channel and/or sill trim.
I use a two piece flashing system. The first piece of flashing is a flat piece that goes against the wall that is wider than the ledger board so no part of the ledger board touches the house.
The second piece is bent like a regular piece of flashing, (3" X 3" or 4" X 4", what ever you have to work with), I like to come out from the house about 3" so I cover the butt where the joist meets the ledger board and go up under the door sill. You might want to run a bead of sillicone starting atleast 6" away from the door so any water that runs down from the J channel, can't get under the flashing.
I don't see the need to use flashing over every joist running out from the house if you are using pressure treated wood. (And you should be.)
If this is an L shaped deck, I would angle my decking from the corner out. If this is a streight deck, I would frame the deck so I could use one piece of decking against the house and butt the decking tight against that piece. (it's going to shrink) Be very carefull to watch the end grain of the decking so it will not cup up!
Currious, If you are going to wall over a window, why would you not use a vinyl lattace to go around the bottom of the deck?