Don't get overly worried about the TX batteries. The voltage drop vs time is not linear. The voltage drops off really fast at first, then levels out for a very long time, going down very very slowly, then it falls off a cliff all at once. What you described is pretty normal.

I don't know about your charger, I've seen different LED behaviour for different chargers. It could be differnet brightness just because the TX is a higher voltage than the RX. Personally, I wouldn't worry about that one.

There are a lot of threads on here about .46 size engines and props for them. If you have the ground clearance, an 11x5 is generally a good prop for a trainer with that engine. The large diameter moves a lot of air, giving it lots of thrust and provides good breaking when you dive or idle down, while the low pitch keeps the airspeed down.