Looks like you are making good progress there. Just remember, it always looks worse before it gets better.
With the rust hand prints......most people don't know that you excrete a form of acid when you sweat. This rusts metal, depending on how much your body excretes (I have it really bad). If you sand to bare metal, clean it straight after with something like Prepsol. I bought a jumbo size drum of Prepsol and wiped over every surface after sanding JAM.
Those that don't do this, end up with really nice paint jobs....but with bubbling (how many of these have you seen!). It comes back to a quality paint job being 90% prep!!!!!
I am a fan of fibreglass. I think it repels moisture a bit better than body filler. Repairing holes with fibreglass can be really good if you can fill the hole with resin. It sets rock hard and does a good job. If you have a hole in a panel, with nothing behind it, fibreglassing can be a little tricky. I would glass behind the hole, then in the hole from the top, in a 2 part process.
You can do this with your rust, but from your description you will need to do it twice (one on the outer car skin, and one on the inner storage bin skin)