The core of the sentence is "Problems confronted the son of Shahjaham." "Confronted" means these problems were like walls in front of him. The first part of the sentence lists the problems. The problems all have to do with a decay or a decline in the moral character of the Mughals. "Retrieve the effeminacy" means "strengthen the weakness." "Put heart into a decaying system" means to make the system stronger, more active. To cure the rot. "Put faith into a listless soul" means to make their souls less tired, less lazy, by inspiring them with faith. I think the sentence is suggesting that one of his sons will succeed Shahjaham, but we won't know which. But whichever one it is, that son will face huge difficulties. "Splendid" power is clear. I am not sure about "cankering" power! But he is saying that Shahjaham was splendid in some ways, but not in others, and that the Mughals had become weak and needed to be inspired. Finally, he suggests that none of his sons were good enough--the problems were so big it would take someone really special, like Mohammed or Theodoric, to correct them.