When I swapped out the Caterpillar 3406 for a Cummins NTC350 Big Cam III (well, Big Cam-ish, anyway) I used aluminum tubing for the straight sections. The couplers to the air cleaners are from the kit, and the 90deg elbows are scratchbuilt from Plastruct elbows and strip stock for the ribs.
Here are the elbows before paint:
With this swap, I got lucky & the kit exhaust part fit with just a little tweeking.