Maybe slimming down intentionally was one of the main problems, he did that when he rode at Cannondale and even durning the next year at Tinkoff his endurance seemed to suffer, at a certain point it was usually lights out for him after a hard race.
Maybe the illness messed up his preparation (he probably just lost water weight because of dehydration, but it can kill your form). Starting your season so early is probably not the best thing to do, but Specialized is probably pushing him to ride in Australia and if they are paying a decent amount of his salary they have some influence, so just skip San Juan.
Despite his (sometimes well crafted) Image he always seemed to be a hard worker, he never was like Pippo, who was always more style than substance and cruised on his talent and his class.
Taking a break right now is the smart thing to do.