I think I have a solution, but it seems inequitable, and too Orwellian.
You forget testing through the UCI. You only need test 60 riders in the peloton, and they should be tested upwards of 150 times each. 10,000 tests.
The top 10 flat/cobbled classics guys. The top 10 hilly classics guys. The top 10 sprinters. The top 10 Tour prospects, Giro prospects and Vuelta prospects.
You test both biomarkers, and traditional blood and urine analysis.
The key is to eliminate the Red Queen Effect, which is the arm's race theory.
http://en.wikipedia.org/wiki/Red_Queen
You prevent the winner from doping, you create a inverted arm's race. That is, if the winner and top tier talent is clean, they will intimidate the new breed from usurping their status with dope.
One of the advantages of doping for the elite tier is it is a funadamental barrier to entry, and the richer you are, the more detailed and effective plan you can afford. Anyone entering the peloton faces a choice, and this already creates a selection from those who do not completely embrace the culture.
No the barrier to entry becomes an effective "clean status". If Rumsas rides into the top tier one year, and has to go clean, and subsequently drops out of the top 100 when he comes under the testing regime, he becomes a pariah, if he was not already. The top tier will intimidate the dopers. Can you imagine Armstrong allowing a doper to threaten his status if he was clean? It would be bizzaro world Simeoni mk deux.
Can you prevent them doping with testing? This is the salient question.
There are studies that exist which indicate hematocrit will never rise more than a few gross points, so how can riders like Armstrong come in at 48% with natural 42 crits. You can test their crit before the startline, not 3 hours before. All bio-markers should mitigate any doping gains.
Once you have the winners riding clean, the process of the Red Queen Effect, is effectively inverted!
How do you know who to test? Quite simple, just poll the managers prior to the start of the season. For the Tour it is simple, there will be no winner outside Vino, Klodi, Valverde, Levi, Sastre, Evans, Schleck, Menchov, Kashechkin, Contador, Rogers. They submit to this comprehensive regime.
Once the process starts to work, the reversal of the culture begins. Dopers will be intimidated. Teams will be intimidated to have dopers winning second tier races. They will understand, that it is no real worth having someone dope to win the Criterium International, and make no real gains towards entry into the top tier, and face the opprobrium of the peloton.
This is effective cultural change. Aradigm shift in doping culture: approbation > opprobrium.