6 mil plastic vapor barrier should be taped at the overlap seam.

If you're going to use 2x10's then they are 9 1/4" tall, and your putting in two 4" layers of foam, which equals 8".
How are you going to deal with the extra 1 1/4"?
You could leave it and add another layer of sheet goods, osb or plywood and then attach your felt and then your 1x4s that way the 1 1/4" gap could be used as a soffit to ridge vent and keep you having a cold roof.
The tar paper will catch any leak through and shed it down the roof, if your 1x4's have cut outs under them to allow the water to drain.

We heard a horror story at a conference about the 1x4's holding the water from draining and the roof decking rotted.

As far as the holes through the vapor barrier caused by attaching the 2by stock that's just something you'll have to live with and it isn't that much to worry about...

Jim Rogers