Oh, head.... Never mind what I said then.
As for Link killing (or not) Ganondorf, yeah, we don't know what happened, but then Ganondorf loses his Triforce Symbol, and Zant clearly snaps his own neck. We don't see him after this so he may or may not be dead. He might escape death again like he always does though if he did die.
Bowser with the Star Rod can resist all but the combine efforts of the Star Spirits nullifying his invulnerability so why not soul attacks. And he can grant himself wishes so he could most likely travel through Dimensions easily.
And I don't see what's so wrong with Bowser getting the Rod just because it's not part of Bowser's basic powerset and the Triforce of Power is part of Ganondorfs basic powerset, and this has nothing to do with the fact that they're both still Artifacts/Items helpful for combat. The Rod is his basic powerset in Paper Mario, just not in any of the other games.
And, clearly, Mario/Luigi is physically stronger than Link if he can throw Bowser high into the air and like 100 feat away. [Answer to ESB-1138 seeing Link to be physically stronger than Mario/Luigi]
Hand-To-Hand, Ganon is faster (unless Bowser is anything like he is in Super Mario 64) but I can't say stronger. But then that part where he wipes out a Sage with a punch, that's lethal. I hope he can hit Bowser with that before getting Burned by Bowser's Trademark Fire Breath though. And without the Triforce to protect him since it's hand-to-hand (if it is), he can't keep from being phased by that attack anymore. It won't kill him any time soon or anything, but he can hit him from afar for a while.