"amazingly bad 3-28"
Hate to be a jerk, but it's actually 2-28!
Anyway, just a quick look at your team suggests a few quick fixes. Right off the bat, your stadium is ill-suited to your offense: Astrodome is death for home run hitters, and you drafted 202 home runs (including Ryan Howard's 58). Lots of money wasted on that offense.
As for the John Clarkson thing, well, that would take some micro-managing to pull off, which I don't believe you're up to at this stage of your WIS career. As it stands, you've started poor Clarkson every game, and since the 5th game of the season he's been extremely fatigued (under 50% for 25 of his past 26 starts). You know that there are performance penalties when players are tired, right?
At the very least, use your AAA to spell Clarkson a few starts, because it's only going to get worse otherwise.
Oof, and I just looked at your most recent boxscore and saw that even your relievers are wiped out (under 10%). I'd strongly recommend starting your AAA pitchers in at least 2 straight games with no pitch count/max, put everyone else on rest (including pinch hitters), and let your rooks get shelled for 9 innings. A few games of rest will help your pen out.