1.you shouldn't need to see the fuel just use the vent pressure line ( the one that attaches to the muffler) as a overflow let the excess go into a jar and pour fuel back into your can or jug.
2.use the nylon ones first, wood ones don't last long on a trainer, using a pencil will not get you a accurate balanced prop most of the guys I know dont even bother with 40 size props one prop strike and its out of wack anyway.if you want to balance your props get a "real" prop balancer if you are going to do it do it right.
3. I am surprised your mount did not come with rubber mount bushings that slide over the ears on your engine most of the Hobbico planes come with them now. they call them iso-smooth mounts check your bag of hardware, if not call hobby services and get one there 2.50 mounting the engine to aluminum with straps looks a little sketchy. I read your instructions and they were not too clear on the hinges or the engine mount didn't even have the mount correctly listed easy to understand the confusion. not to pile on but no less than 3 hinges for rudder and 6 for the elevator.