1. Might not fit with some pinion & spur combos due to the large diameter of the gears- I wouldnt worry, 99% of us dont use gear covers and I've only seen one case of a stone getting caught and killing the esc as a result.
2. Lipos = win
Bear in mind resting voltage will be higher/rebound a little than when you are running the truck.
3. I doubt your eyes can tell the difference between 45 and 50mph
I always thought my hvmaxx setup was pushing my gmaxx along at ~35mph, but in reality it was only ~20mph, once I did the sums on the calculator. You need a GPS or radar gun to get an accurate idea.
4. Good for you, but make sure the velcro doesnt come unstuck from the chassis (I would get the optional holddown when its released).
5. We're in the UK dude, its like 2*C outside! I would get a proper IR temp gun though for accurate readings, but your findings so far are excellent.
6. The caps on the esc will hold a charge for quite a while, so they wont recharge every single time you connect the lipos, which is nice (sparks make me nervous, reason why I didnt want to learn how to weld at school...).
7. Truck stops moving. Sometimes it may become jittery on the throttle, or so people say, but usually the truck will simply grind to a halt. You will see it slowing down as the lipos begin to dump though, so you will usually stop running the truck before the lvc kicks in.
8. See above. the discharge curve of lipos is very flat until the last 30 seconds or so.
9. Depends. If you plan to use the truck again in the next few days or so, then charge them up fully. If you dont plan to run it for a week or more, then a 'storage charge' of ~3.7 volts or so is recommended. You should have that feature on your hyperion, if not you can simply stop the charge once the voltage of each cell is roughly 3.7v also- you should be able to see the individual cell voltages if you press the right button during charging, see your manual.
Fun fun fun...