Well, you could turn the water back on now that it's not raining and see if the leak starts up again..

Assuming asphalt/fiberglass based shingles, probably he applied a roofing cement - silicone sealants generally don't work well with roofing. When you do a repair or in your case a retrofit, often the shingles are too fragile to pry up to put nails for brackets under a tab. The choice is to risk breaking or tearing a tab clean off or putting a small neat hole through it. When I've done work on my own roof I just went right through the shingle. After, if I could break the shingle seal and carefully hold it up I'd put a dab of roof cement where the hole was and mash it down until the dab filled the hole in the top layer. If I couldn't get the shingle up without breaking it, I'd just very carefully apply the cement directly to the hole with the tip of a nail. Concerned about a black dot - just take a handful of roof granules out of your gutter and dust the area if its still tacky.

I'm not a fan of roofing cement but it's nessary on exposed nail heads. The needles might very well deflect water enough to cause it going beneath shingles.

Wood screws from the inside - length needs to be more than 1/2 inch but less than the plywood plus sheathing. 3/4" would work. One at each corner and a couple in the center will hold it.