A rigid mounted Norton twin engine will in my experience never be as smooth as a rubber mounted engine on the street and cruising, unless the rubber mounts are shot. However, if your Atlas crank has never been re-balanced from what came out of the factory, getting it balanced for the weight information Jim provides for the rods and pistons he sells it should be one heck of an improvement.
Where I think Jim's long rod conversion parts shine for me is when the engine is getting close to or hoovering at max HP. At around 7000RPM my engine feels smooth strong and like it is just getting started. Your performance will depend on a lot of other factors though. I have a lot more in my 750 P11 engine than his long rods and pistons. If just making the long rods and pistons change, I think it will smooth out some as long as the crank is rebalanced. Basically, what I said in that paragraph above and what Nigel said earlier.
Andy Molnar uses 75% BF for a rigid mount. Jim is similar for a rigid mount maybe 72%. Ask him.
What other changes do you have planned for the motor when doing the rods and pistons?