The dual exhaust will certainly help you.
Fall of 2003 I kissed the #4 piston with its intake valve, denting the piston face, bending the intake valve, bending the pushrod and putting a bend in the cam. We didn't know I had done so much damage until we took it apart.
The 78 did not run right after I had jumped timing and did all that damage in a split second, and at idle I could hear a difference in its sound between left and right side and also feel a difference when placing my hands below the exhaust pipes.
We rebuilt the 350 and then still had trouble getting it to run smooth so I sent the carb off to Texas to be rebuilt by a master. When the carb returned, we STILL had trouble getting to to run smoothly.
Kenny got busy at work so I sent the 78 to an older mechanic who has years experience building race engines and he had just as much trouble as us, but then he took off the valve cover and found that one of the rocker stud bolts had broke...and that was our trouble. He replaced the bolt, checked the broke-bolt spark plug and also checked timing. Now the 78 is running smooth as silk and has lots of power.
With the first and second problems, the symptoms were virtually the same. The engine would not run smooth, I could definitely hear that something was 'off' and at idle it was very noticeable; both by listening and feeling the air puffing out.
Good luck determining what the problem is. I wonder if a compression test would help? CT is how I found out about the first problem with #4/intake. I imagine you could also pull the spark plugs on the side the exhaust sounds funny on to determine which one is having problems.
Heidi