You cannot move the chambers "back", it will make the tuned length so long that you will probably never get into the powerband. The tuned length is cqlculated from the exhaust side of the piston to the middle of the divergence cone, make it shorter and the powerband comes on sooner, make it longer and it will come on later-to long and it may never make more power. Change any of the angles of the pipes and you change the power delivery charracteristics of the pipes, or you could just make junk and have a bike that is un-tuneable.
The most expensive part of that bike may be the proper pipes, shit pipes equals shit performance.
I am currently working on a set of "up" pipes for another project using a known, very proven dimension for the Rd400 engine, they will not be done till mid winter however. If I had a paying customer, I could move this project up in my schedule.