Find something that demonstrates ancient bacteria were not so different than a current strain today, and this is dismissed because everyone knows ancient bacteria MUST BE different because ToE says so.
When you've accrued such a weight of evidence for a theory that you have to be ignorant, or ideologically motivated, to reject it, then yes. You get to use the parts of the theory you've so substantiated as essentially fact.
Doesn't seem fair? By all means, I invite you to establish a similar weight of evidence for creationism.
The conclusion is taken as fact, the molecular clock angle, and so any data that disagrees with that conclusion must be contanimation even if the best measures were taken to prevent it.
Yes. That is because there is a million times as much confirming evidence for the molecular clock models as there is disconfirming evidence. And we do know that, despite our best human efforts, contamination does occur sometimes.