Position the silencer such that the inlet is only about 1/4" away from the frame to leave ample clearance for the shock. Line up the tail of the expansion chamber with the inlet of the silencer and make sure that the expansion chamber doesn't interfere with the kick-starter, frame, carb or coolant tubes entering/exiting the water pump.
Once the silencer is mounted, you can trim the length of the expansion chamber tail until it all fits together. Again, trim little bits at a time until it is just right. It is much easier to trim a bit more off than to try filling in a gap with your welder.
I rotated the tail 90 deg before welding it on so that the threaded mount is pointing straight up when mounted on the bike. This should make it easier to make a mount to the frame.
At this point, the exhaust will be finished except for the mount that goes on the very bottom of the expansion chamber. This last mount will be added after the cradle is built.