What I am doing is no different than what you are

You are assuming that SF would go on an extended drive the opening series to give this "gassed" defense a rest and then assuming again that whatever rest they got would be enough to hold the Chiefs to exactly the same production SF got out of their drive.

You're correct that the other things all certainly contributed to the loss, but the fact is they were tied at the end of regulation with a chance to win the game and he bungled the decision.

I also disagree with you slamming their defense as much as you are. They held KC to 19 points in regulation, forced 2 turnovers, and were put in an awful spot by the special teams misfortune. As you have noted they were banged up in the secondary and lost Greenlaw early and his replacement was absolutely torched in coverage. I can't hammer Wilkes too much, I thought the defense played well enough to win. The offense had ample opportunity to end the game with a Moody FG try and they failed to convert a first down. SF also got no help up front from the Bill Winovich led crew.
There were at least 3 holds on key plays for KC not called that were apparent. KC was called for holding the most times in the regular season yet managed to play a "clean" game in that regard. The D gets a pass from me. Shanahan and the offense lost the game for SF.