The whirring noise could be idler pulley/tensioner pulley/water pump pulley or maybe the power steering fluid is low. I would remove the belt and start it up, see if the noise is gone. If so, then its a belt driven issue (pulley, pump, etc...) If not, it could be the transmission.
As for it not revving up past 3500, its designed to do that. If the trans is in Park or Neutral, the Powertrain Control Module limits RPMs to 3500. As long as it goes past 3500 while in gear, your OK.
So the noise goes away in second gear? Does it come back in 3rd or 4th? Will it do it in first gear if you let off the gas or only while accelerating?
I'm sorry. I work on these things all day, and my mind has drawn a blank. Diagnosing noises over the internet is very difficult! I'm going to opt out, and if another expert has any suggestions, they will chime in.
Good luck, I hope you find a resolution!