Electrical – Grounding Wire to copper pipe for cable

The instructions for the fixture are only correct for a metal box. If a metal box was used, the box itself would (should) be grounded. The bracket that holds the light would then be connected to the box, which would make the bracket grounded. Finally the ground wire from the fixture would attach to the bracket, grounding the fixture.

In the case of a plastic box, the box is not grounded. All ground connections must be made by connecting the ground wires together. So in your situation you are correct, you'll connect the ground from the supply to the ground from the fixture using a twist-on connector (or other approved connection).

That looks perfectly suitable. One additional thing you should be aware of, though - if your existing plumbing contains any yellow brass fittings, they really need to come out because of a chemical quirk of PEX; the zinc gets leached out of yellow brass, leaving behind only soft copper, and the fittings may either leak or plug solid. You can use RED brass, just not YELLOW brass.

The manifold should be one size larger than the pipe supplying it.

If there's any question at all about grounding, a solid ground rod can be driven... with the result of giving you a better ground than you ever had by grounding through copper pipe.

Like copper, PEX requires a 1/4" drop per foot (never install it level or wavy), and requires a drain at every low point so the house can be winterized if necessary.

Is there any particular reason for going with PEX instead of tending to leaky fittings as you find them? I suspect that those fittings were always leaky because they were never sweated together correctly in the first place. I ask this question because replumbing the entire house in PEX is really a large, expensive job... while replacing (or resweating) one fitting at a time is relatively cheap.