Inverted 4 Strokes
You shouldn't have any problems with the inverted four strokes. I have used the OS 91 and Saito 72 inverted. The engine doesn't have any idea which direction it's facing, however the only drawback I've found is trying to reach the glow plug. If you have a cowl, I suggest using a remote plug or onboard glow. If not, you just have to reach a little more during starts. You might also look at using a single point fuel system inorder to keep from flooding the engine.
I think regardless which mounting method you use, the engine break-in and needle valve tuning is much more important than which way it's mounted.