Darren:
Broken shafts on FE valvetrain are most certainly not unheard of. As spring pressures and RPM rates escalate it's going to be a potential downfall of the design, that being said think this through. Two things come to mind in reading this and looking at your pictures.
1. Are you certain the stud is secure in the head, is there any chance the threads have pulled in the aluminum head allowing the shaft to flex a minor amout before fracturing? If not read on.......Roush buys the complete Rocker Arm sets from Harland Sharp and uses them to assemble their engines.
2. While Roush is only willing to "Sell you at cost" a replacement set, and since it doesn't appear there is any other visable damage to the valve train other than the fracture in the shaft. AND since Roush is really doing "Nothing" for you warranty wise, (??) why not go to Harland Sharps website and purchase the rocker "Shaft" for their price of $120.75 and save some cash?
Keep an eye on the rocker arms themselves, aluminum when used in a rocker arm work hardens with continuous heat cycles and can become brittle, it is used for this application because of light weight and ease of machining, but is not the best material for the application. While you are repairing this it might be prudent to check ALL the rocker arms individually and the bushings for any sign of galling or potential cracks at the bottom of the bushing bore or at the tips where the pin is secured, and inspect the other shaft as well. Occasionally the pin will begin to migrate in the tip and can cause REAL problems. Retorqe all fasteners and take the wife to dinner on the $$ you saved! It's not a difficult task.
Good luck
http://www.harlandsharp.com/components1.htm#Shafts