further testing shows me that it works even without the transformer. I get to return that too now 
Technically , a PSU labeled as 2500w on 240v should do just fine on 110v for an S9k which does not consume more than 1300w , but you should still be careful, just because it worked for a while it doesn't mean you should return the transformer right away, electricity related issues need a few hours and sometimes days to start coming your way.
so for the fan, I just swapped the intake and exhaust position both on the ends of the miner and then it's location on the control board.
Thanks for the update, although it does not really make sense technical wise , but my thoughts are, one of the fans' wires was a bit loose, when you swapped them you secured them right and, bingo! , proof is, if you were to put them back in their original places, the miner will still work ( I would do that out of curiosity ) but I know many people wouldn't.
next step is to figure out sound proofing and ventilation...
There are plenty of topics in regards to ventilation and sound proofing, before you start your own thread, please search the forum similar topics.
Good luck.