It seems as in 2000 and 2001 there was certainly a split in the peloton. Those who used blood manipulation and those who didn't. Actually i read reports of race doctors who claimed that in the spring of 2001 the peloton was as clean as it hasn't been in along time. However, for the Tour this changed again and some teams restablished blood manioulation methods. I leave it up to you to guess who that was.
As for Ullrich, remember that after the 2001 season he got in all those private and mental problems. Ullrich at that time was very frustrated. He realized that if he wanted to won the our again, he had to go bike in the the doping cycle.
By 2003 we must asume, that blood doping of some sort was totally reestablished and almost everybody in the peleton used it again.
However, it seems that there was still something of a two class system and not everybody was riding on the same good stuff.
In May of 2006 a telphone call of Rudy Pevenage with Fuentes was recorded by the police. In this telephone call, Pevenage seems to be suprised how good a certain method is working and talks with Fuentes about using this for Jan.
So while we must asume that Ullrich worked together with Fuentes before 2005 it seems that Ullrich in 2006 seemed to be willing to use a certain doping method which he hadn't used in the years before, but was apperently already known and used to some parts of the peleton.
In 2006 Ullrich wanted to have a real competitive situation once again. In what he wanted to be the last year of his career, he was willing to take risks again. In that year we would have seen the real Jan again. A Jan which was on the same doping level as his competitors. He would have smoked everyone like he did in 1997.
Of course at the end, Ullrich is a drug user just like other, too. However, taking a closer look at the story, Ullrich is more of a victim than a profiteur of the EPO/blood doping era.
As Jeff D'Hont said, one of the guys that knows more about the peloton and the drug abuse in it, than must other people: "If the peloton was clean, Ullrich could have won the Tour 10 times. He was by far the most naturaly gifted rider"