I suggest you put it in right away, just so it runs better. The blueing of the pipes is not as big of a factor on the Speedy/TBA cause they have shields over the exhaust headers unlike the bonnevilles and thruxtons.
In regards to breakin, I was instructed to ride the bike at all different speeds so that it does not bet broke in at one riding situation...so ride at 35 for awhile, then bump up to 55 and back to 25 and hit it at 75-80 for awhile. I did this for about a week and had no problems.
