2. Front windows. I had a pinhole leak around one of the windows. Unfortunately it occurred while I was traveling. I tried twice to seal the leak with big ugly globs of chalk. After two failures, I sealed around each window with gorilla duct tape. At the end of my trip, I stripped all the chalk and did a final repair.
Caulking is really a secondary seal. The primary seal is the putty tape under the item being sealed.
It is usually a poor primary seal that eventually causes the problem. The only real way to rectify the true problem is to remove the item in question, properly seal and then apply a new secondary seal.
A lot of times with windows, it is installer lazyness/production speed that doesn't get the window centered to maximize the primary seal around the perimeter. My father once removed a window that had a leak and the problem was the window was set in place and shoved to one side. This caused there to be almost no overlap of the window and the framing on one side and the top. By taking a couple minutes to shim the window so it was centered in the opening, he achieved a minimum of 1/2" overlap for a decent primary seal.
In regards to your question of checklist, it's very simple. If it isn't a single piece of material, it is subject to a leak.