geish,
First things first. Welcome to RCU and RC flying. Great hobby with a lot of terrific people.

Second, do not try to fly alone. It is much more difficult than you might think, and I don't want to see all your hard work destroyed after 20 seconds in the air.

Find a local club. They'll have instructors who'll help you learn to fly. No cost and they'll keep your plane in one piece.

Now on to the plane. A Piper Cub has some idiosyncrasies that don't make it all that easy to fly. You'd be much better off getting a trainer to start.

Okay. Your questions:
1) Mounting the engine inverted. You've gotten good advice. Do watch the height of the tank; once the fuel gets flowing, your tank will empty itself through the carb.
2) As Jetts said, 150% airflow out. (If you cut a one inch hole in the front of the cowl, you'll need three inches in the rear.)
3) Your engine is broken in now. Not much you can do to change that. BUT, it sounds like you did everything right, and the fuel you're using is fine too.
4) Get the pushrod as close in on the servo as possible, and as far out on the engine's throttle arm as possible. This will keep the throw as short as possible. Then you can try other stuff if it's not enough.
5) Refer to #3 above.
6) See #1 above. You normally want the center of the tank to line up with the throttle barrel. It most likely won't be possible mounting inverted. But you will need to be careful about fuel syphoning out the carb.

I'd recommend mounting the engine on it's side, or at a 45 degree angle. It'll be much easier in the long run. Both for running, and for the fuel issue. As a newbie, you need to reduce potential problem areas.

You never mentioned the muffler either. Did you get a "Pitts" style in-cowl muffler. If not, you'll have to cut a hole in the cowl for the muffler to stick out anyway.

I wan to say again. GET AN INSTRUCTOR!
Joining the AMA is pretty much required to fly this size plane. It will almost certainly be a requirement to join a local club.

Here's a link to the AMA site. http://modelaircraft.org/templates/ama/

Good luck,
Dennis-