I have several planes with inverted engines. Starting and running them is no more or less challenging than any other orientation. The key to starting any engine is to get a good prime. The key to running an engine is proper tuning. Learn how to start and tune an engine and you should be able to operate it any way you want. When the engine is inverted and cowled access is a bit more difficult. While it's true that in theory the glow plug could be sitting in the sump that someone else pointed out, and flooding is often quoted as an issue, in practice, it's actually quite difficult to flood an inverted two stroke. The reason for this is simple. Any excess fuel that comes out of the spray bar and into the carb is going to drip on the ground, not into the engine.

Having said all this, why are you installing a screaming 2 stroke with a pitts muffler in a Cub? There's an unwritten law that only 4 stroke engines should go in Cubs! If you go with a 4 stroke, the muffler will be significantly smaller and easier to deal with.