Great response flygilmore, but alas, not an answer to the question at hand.

to get back on topic:. What is more important, to tune the pipe to the engine, or to fit it in avaiable space. If you want to fit the contraption into available space, it is no use to ask about the consequences. You will find out about that soon enough.
If you want to do your engine a favour, use the 11" header length, and adapt your airplane to fit the items that your engine needs to operate to it's full potential. There are no if's and but's. Just do as you choose, and accept the results.