>> How does acuisiton noise influence the BER/TJ measurements - is tere an established way to calculate those effects out?
Acquisition noise is always tricky. In my experience it's worse on real-time scopes than equiv-time scopes and BERTs. To subtract it out you have to make assumptions about how it's distributed. If you assume the noise is Gaussian you can come up with techniques to remove it, though it's never clear how that affects your systematic uncertainty.