Most of your standard trainers and high wing planes have downthrust. The reason is because the wing is on top and creating drag. That drag is pushing back on the leading edge of the wing. Push the leading edge back and the nose of the plane comes up. So, downthrust is usually required.

Most low wing planes are opposite. The drag on the leading edge is pushing the wing back, but since it's on the bottom, that will tend to pull the nose down. Up thrust is needed.

Shoulder wing should come out with zero thrust up or down.

That's just the theory. Does it always work? I dunno. Ask an aeronautical engineer.

On the rubber:
Sounds good, in theory.

But consider this. By the time you get the bolts tight enough to secure the engine to the firewall--you will have completely smashed the rubber. It will not provide any vibration isolation after it's smashed down tight.

Forget the rubber and mount it directly to the firewall. Gas engines shake. Nature of the beast. You just make sure the airframe is glued correctly and add some tri-stock in strategic locations up front to prevent any flexing. You want a solid firewall and mount. The vibrations will be transferred through the airframe. The wings and the mass of the airframe will absorb the shock from the engine vibrations.