When it comes to replacing shingles, use ribbed nails. And don't nail them near an edge. Old shingles splinter and crack much easier than when fresh, so don't use the old nail holes as guides.
In regards to roof leaks, the obvious and best solution would be to crawl up in the attic while it's leaking and find the spot. Measure to the walls and scribble down a little map. If it's actually a hole, take an unbent coat hanger and see if you can push it through so you can find the spot from above. In lieu of that, a long nail.
If you have a general idea of where the leak is, you can certainly simulate a rainstorm with a garden hose and sprinkler attachment. Just set it on the roof and let the rains begin.
If the leak's big enough, you might be able to see a pinprick of light coming in the dark attic when the sun's overhead.
And you can't be sure of a roof leak's location by where it comes in the house. You really need to inspect the underside of the roof, itself. I saw one case where a leak landed on a board, ran to the side, crept five feet down a 2×4, down a metal conduit, down another 2×4, and ended up coming through the ceiling about 15 feet from the actual leak.
As always, caution is urged when working on roofs. No flip-flops, please. If you're doing the garden hose routine, stay clear of the wet areas. Wet, moss-covered shingles are like glass.