I'm not sure if I understand why you can't use the express VI. I don't recall seeing a problem with over 2048 data points coming into the spectral measurements express VI, and I have confirmed this as well. Any VI using the FFT algorithm will perform slower when using a number of points that is not a power of 2, but in this case it is still possible to use the FFT VIs.
Is there something about your problem I don't understand? Have you tried to use the express VI and gotten an error? Are you experiencing strange results with the express VI?
As far as the frequency being incorrect, I suspect this is because your data does not include time information. In other words, what is the time (dt) in between your data points? The easiest way to generate an FFT with accurate frequency is to use the waveform data type, which includes timing information.
I hope this helps. I'm sure that we can work on this together and find a solution.
Casey Weltzin
National Instruments