Rocker, I think the WD40 was mentioned as a product than can be used to remove roofing cement from one's hands, not as part of the repair itself. The best long-term method for fixing leaks is to find the exact source of water entry, and eliminate it (usually by means of re-directing the flow and closing the entry points). If your place has a steep pitch, you might consider paying someone to perform the repair, rather than risking a tumble (Ouch hurts!). Either a professional roofer, or even a skilled handyman with good references.
In the last 40 years, I've installed many skylights, and never had a leak. But I've inspected dozens of other people's installations (while doing home inspections), many of which did leak. The common problem with most of the leakers was improper flashing, either at the junction with the roof, or on top of the curb/lightshaft walls. One classic leaker had absolutely no flashing at all. The lady living there just accepted it, and lived with empty buckets in her bathroom, ready to catch the deluge every time it rained.