In my opinion, the only way to do this job right is to tear out the
both layers of roof and start from scratch.I don't know if I got a new
skylight if it can be installed below the old shingles without
damaging the new shingles up there now.
My roof is still in good shape with no issues. I would hate to start
opening up a can of worms by replacing the skylight, plus money is an
issue for me right now.

Is it possible to tear out the old caulk/gasket surrounding the glass
window and recaulk or re-seal? Is there a special caulk for skylights
or is it statndard caulk?

I know the leak is coming from the seals. If I could somehow just re-
seal it, that would solve the leak. And also what if I tried to seal
those holes from the inside, would I make matters worse.

Thanks again for all your inputs.