Roelof is correct, the length and shape of a pipe is designed to give a certain amount of back pressure which stops the fuel from flowing straight through the engine. There are no valves on a 2stroke engine, so fuel input and exhaust output is all done through ports in the cylinder sleeve as well as the crankcase.

Nitro gas engines are nothing like your everyday car engine, car engines are designed to be very forgiving to dealing with parameters outside its optimal range, a nitro gas engine is not, its is more like an F1 car engine, in that it is designed to very high tolerances and will not like to work much outside its optimal range.

There is possibly one thing you could do that would not upset the engines balance too much, you could cut the manifold so you can rotate the output by the required amount, sealing with silicon tube and zippy ties, if done correctly you would neither lengthen or shorten the manifolds length or dimensions. This would change a forward facing pipe to one that sits at 90deg to its current position. You would also need to manufacture new mounts etc to support it, assuming that there is room to do this to begin with.

Your next problem will be car handling, as you have just upset the weight balance of the car, by moving weight from the side to the rear, so how it drives and turns will be different, you might need to add weight blocks to the side that had the exhaust previously to fix the left right balance of the car and maybe move some weight forward as well to help with turning if thats a problem.