i have also heard of the '03 cobras breaking t-56's. however it is not with the stock power. if i remember correctly the input shaft isn't quite as beefy as other t56's (ie viper) and breaks around 550hp.
as for the 3650 vs. t45 debate, there is NO way the t45 is stronger. it just doesn't make economic sense for Ford to swap to a heavier, more expensive, tranny that is weaker, or for tremec to redesign the 3550 (to make the 3650) to be weaker than the cheaper t45.
-steve