Thank you for your kind words, I'm glad we have been able to help you.
Installation of the front door will depend on the brand of door you purchased, and the sill that came with it. I know this not a fair question for one guy to ask another but, did you look in the directions to see what is required?
Now, as far as the deck is concerned, drop it down a step. When you get a few feet of snow on the deck and it starts to melt, it will be looking for the fastest route. That will probably be under your door! I would want mine about 7" above the joist. Then adding the 5/4 decking , (if that is what you intend on using), you will have a comfortable step.
What kind of door are you planning on having there, (don't say slider). Can you say "Put some towells on the tract, quick!"
I install flashing from below the door to just below where you are going to hang the deck. then I install flashing again, down from the door, then angeled on top of the joist, and out about 3". That way, there is no chance to have any water get behind your deck and rot your sill. Install a wooden kick plate over the flashing, under the door.