I have an aftermarket rear exhaust it is a 3 chamber but I am running it on a side exhaust engine which you can image causes a huge length in tubing to get from motor to exhaust. Am I creating a problem by doing this?

If you increase the length in between the manifold and pipe, the engine will get better low rpm power(more torque) but you will loose high rpm power(less rpm at full speed).
If you decrease the length in between the manifold and pipe, the engine will get better high rpm power(more rpm at full speed) but you will loose low rpm power(less torque).