To stop this roof leak, this skylight needs to be reflashed. The skylight can be maintained to save on costs.
Boxing in this section of the roof with siding makes the most sense.
The height of this pipe may need to be extended upward.
Repair vs Replace Roof
The rear gutters need to be repitched and a downspout added. This will prevent these gutter guards from pushing up the shingles.
Proposed Gaf Timberline Weathered wood shingles.
Visual Marketing By Lead Symphony – Patent Pending