I have never heard any connection w/ Pujols & Balco.
The one big story I remember about Pujols & PEDS was when former major league player Jack Clark who said Pujols' ex-trainer used to "shoot him up" with performance-enhancing drugs. The trainer Chris Mihlfeld, denied the charges. Albert said he was going to take legal action.. Suddenly Jack changed his story and he and his co-host Kevin Slaten (St. Louis' wanna be sports talk shock jock) both were fired.
More on that story here:
http://m.mlb.com/news/article/56426970//
The biggest questions I remember hearing about Pujols is that he was a lot older than he claimed to be. That's why he lasted until the 13th round. The age concern and the fact that he didn't have a "baseball body". Not that he was fat per say, just didnt't look like your prototypical major league prospect. Lucky for St. Louis they took a chance on a "fat kid" who could hit.
I like to think he was/is clean but to be honest nothing would shock me anymore. But until someone can show me absolute proof I am going to give him the benefit of the doubt!