There is no communications between TSA and the airline about anything you have in your bag, unless you have something you shouldn't. The X-Ray screener is pretty glued to the screen, and is not looking for jewels. I know the TSA is not always, um, well, let's just leave it as we all know how the TSA can be. But to suggest they were in cahoots with the airline to find jewelry really is a conspiracy theory. In short, it never happened.
As far as there still being overhead space, something's not right with that. It sounds like the flight was full, and the agent probably assumed that toward the end of boarding, the bins would be full. The should have waited until they got word from the flight attendants that the bins were full, before they started checking bags.
On the seats, there probably really was nothing left available at the time you checked in. You are assuming that those seat were open all along. It's very possible that the people assigned those seats missed the flight. The agent was giving you the only option of sitting together at the time you checked in. Once you board, if someone misses the flight, they have no way to start going down the list of those who got separated.
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