Are we talking about the Chinese 2 stroke engine?
Custom made intake manifolds have been made by builders needing them for clearance and other considerations. Your idea might require that you fabricate what you need or modify a stock manifold. Not difficult if you can weld or solder.
As for cutting into the clutch actuator cover or engine case here's where you might get into trouble. The clutch linkage/actuator cover is held on with three screws. The bottom one is just about where you'd need to cut. Not a good idea because the cover is an integral part of the actuator. It is possible to get a lot of downward slant to the chain and if I understand you correctly that's the direction you want to go. But I wouldn't cut or alter the clutch actuator cover by removing that bottom screw. I hope I understand your mounting idea. It sounds like you want to mount the engine behind the seat? It has been done but the one I saw utilized a jackshaft whereby the engine drive chain drove a shaft with sprockets that then through a second chain, drove the rear wheel. Strange, but possible.
Tom