Okay, let's start with the easy part: defenses.
Don't start SF this week; the Seahawks are very good, and even better at home. SF will stifle Marshawn Lynch, but they won't shut him down completely. Same goes for Russell Wilson: the kid's just too good.
Definitely go with HOU against Minnesota. JJ Watt: difference-maker in so many ways. Minnesota's offense is all Adrian Peterson. Houston will get to Ponder for a handful of sacks, and Peterson will have a decent day but not enough to bench the HOU defense.
I wouldn't bench Jamaal against the league's 23rd-ranked run defense. Charles only had 9 or 10 carries last week because the Chiefs only had the ball for all of 3 minutes. Seriously, did the Chiefs EVER have the ball last week? I think Charles will be just fine.
That being said, I see you have Reggie Bush there as an option. Between the two I would start Reggie Bush. Defying all conventional wisdom, he has once again turned it up and earned lone-back duty in Miami. Not only that, but the Bills are asleep at the wheel on defense. I wouldn't be surprised if tomorrow was Bush's biggest fantasy week of the year.
This is absolutely your toughest choice. You've got two QB's who both have something to prove. Kaepernick time and again has shown he's a great QB this season, but every week it seems "experts" project him to fall apart at the seems. Then there's Eli: fighting for his postseason life. I honestly think you would do fine starting either one, but if it were me I would have to go with Manning. This time of year is routinely when he plays his best football. Hopefully last week's terrible performance will just add fuel to his fire.
Good luck beating your nemesis!