Answers

Without knowing the specifics of the skylight brand and condition, we would not be able to answer the question with confidence.

We use Velux skylights. During re-roofs, we typically find most skylights are not in good condition and/or were not installed properly. 

Both, more than likely. The mason should replace the masonry products and the roofer should work with the mason to achieve a regletted counterflashing and flash the roof under counterflashings.

I would reccomend you seek advice from your local department of labor.

Masons would install mortar on bricks.

Metal roof pricing ranges on what the structure details are (steepness, valleys, penetrations, wall flashings, chimneys, etc.) and what gauge, profile, ventilation and snow retention (if any) is needed or requested.