Brent, sorry your having all these problems! I've been there and FE's can be a trick deal with. This is nothing new as I read before that someone had suggested checking the tolerences between I/E valves at full lift and the geometry of the pushrod cup to the bottom of the rocker arm. This could be the cause of the broken pushrod pieces you describe. I'm assuming or don't remember reading whether you have enlarged the pushrod holes in the intake sufficiently to accomadate the pushrods. If they are hitting but still operating you willnotice a small "wear" mark on the pushrods making contact.
Lastly, I will be more than happy to exchange a fresh, test stand only 428 with completely rebuilt 48 IDA webers (tuned and runs well) completely decked with the goodies for your engine, as is.
Best of luck and hang in there. Once you finally get it right it will be all worth it - I promise! I just got back from the Atlanta chapter Club mountain drive with 6 other Cobra's.