Step 2: How to get those roofing nails out!
Now that the leak point has been found (hopefully), a couple of shingles will have to be removed.
To remove them, reach under them with a pry bar until you encounter the nails.
Not too hard with a newer roof. But with an old roof and bad shingles, another story. I ended up tearing away portions of the old flimsy shingles to get to the nails. Why not, they are going into the trash anyway.
Two problems with removing the nails, not mentioned elsewhere:
Often they are driven really deep into the shingle, since the roofers use pneumatic driven nailers. Not easy to get your nail puller under. So I went into the attic, under the roof work area, and found the roofing nails protruding about 1/4". On my target shingles, I drove the nails out, so they were easy to find and remove back on the roof. Be sure to remove all the nails that drive out!
It is really easy to tear the tarpaper underlayment when messing around with the sharp pry bar. All the more reason to tear away the old bad shingles first, so you see what you are doing.