PJ, I'll take a shot at answering your question of what changed. I guess my answer could be applied to all of drag racing and not just Pro Stock. I think it's because the stakes/bar/ante was raised. To help get my point across here is an analogy using martial arts and street fighting. In my martial arts training we always talk about avoiding street fights at all costs. The main reason being, you never know how far your opponent is willing to go and how high the stakes will get raised. If you start beating him up, to try and get the win, he might pull out a knife or some other weapon. If you pull a weapon or find a weapon to even things up, just like that the stakes have been raised. If you both have small weapons and you're still winning the fight, he might pull a gun. Again, now the fight has escalated to a whole new level. How does this relate to drag racing? Let me explain.
There are 3 basic keys to being successful in drag racing. 1., hard work 2., knowledge and 3., money (not necessarily in that order). As drag racing has evolved, racers continue to raise the stakes in 1 or all 3 of these basic premises. Either working harder than their opponents, gaining more knowledge than their opponents, or out spending their opponents. Racers who do all 3 at the same time are usually the ones who become champions. What happened between 2003 and 2007 where you can see a big drop off?
2003 27--26--27
2007 19--21--20
KB racing, the Summit team happened. A 2 car team, with vast knowledge (Anderson worked with and learned from Warren and Kurt Johnson for years, Line with all his NASCAR experience, etc.), hard working, and some of the deepest pockets in Pro Stock.
2003 Pro Stock Champion - Greg Anderson
2004 Pro Stock Champion - Greg Anderson
2005 Pro Stock Champion - Greg Anderson
2006 Pro Stock Champion - Jason Line
The KB team raised the stakes to a level never seen before. Every team in Pro Stock had knives and KB racing came to the track with guns. Now almost every Pro Stock team has an in house engine program that has guys working 'round the clock trying to find 1 horsepower here, 2 horsepower there, etc. outside of the crew that travels to the races. Warren and Kurt Johnson have the knowledge and work hard but they don't have the money/resources to compete at the level that it has been raised to. Jim Cunningham on the other hand, literally won the lottery and decided to go Pro Stock racing. Just living the dream, he has the money but not the knowledge and I'm sure since he's retired, he's not looking to work 18 hours a day to be successful.
Don't take this as I'm blaming KB racing for the low car counts in Pro Stock. I'm merely pointing out that the bar had been raised by them. If it wouldn't have been them, then someone else would have. The same thing has happened in the other classes as well. Take a look at the guy/team who won the most Funny Car championships from say 1990 to 2004. This team raised the stakes to unheard of levels. Multiple crew chiefs, 2 car teams, 3 car teams, 4 car teams, building some parts in house, now building all parts including chassis in house, etc. You pretty much can't win championships in nitro racing anymore unless you have a huge shop/warehouse located in Brownsburg, Indiana!

Again, I'm not blaming, just merely pointing out.