"How has NASCAR kept a lid on these "special weapons and tactics" missions for 60 some years?"
Well that's a fair question and one I can't answer. Up through the Eighties, before the sport broke into the big time, Bill France could probably slip someone a few dollars to keep their mouth shut. I don't think they seriously try to influence a race very often. I don't think anyone really put an effort into gaming the system until Richard Petty reached 198 wins. I love the man, but those last few wins were hard to reach, and the fact that they stopped exactly at 200 raises my eyebrow.
I don't think Bill France used the nuclear option many times, but Brian France is struggling to keep the sport on top and may be more desperate. When NASCAR was at its peak there was that story about "The Call" that was squashed quickly. They have been known to punish journalists and nobody would have wanted to open their mouths and get kicked off the gravy train back then.
Princess Sparklepony's Daytona pole got a lot of positive press. But if I were Brian France, I wouldn't have used that weapon in the first race of her first full season. I would have waited a year to see if she could put up reasonable numbers to keep the story going. Given her poor performance for the rest of the year, it looks like somebody pulled some strings. But I don't think that was fixed. I think she was excited, ambitious, and got lucky at a place where luck plays a big role.
I don't think NASCAR favors one driver, team or manufacturer. I think they play all the pieces for the best publicity. It's possible that the inspectors are mentioning little inconsistencies and are being told to ignore them and wait to see how the affect the competition. No penalties are being handed down until the folks in the trailer have made their decision. If the guys in the trailer begin to look like they're playing favorites, they announce a huge fine and suspensions. Then it goes to appeal and those are reduced. They've played that a few times though and probably won't get away with it much longer.
I don't think that NASCAR wanted six championships for Jimmy because he's not one of the more popular drivers. But they will want seven, and I think they'll try to make that happen in 2015 and beyond. It would help prove that the sport is just as good as it was at its peak. Tell your grandchildren that you watched Jimmy Johnson, one of the all-time greats. I think there will be some skullduggery to get that 7th championship. Brian France is a complete idiot if he let's Jimmy rack up more than Richard and Dale though.