Is it possible to extract peak locations in the time domain using help from fourier/wavelet analysis?
You can figure where the peaks would be if the other tone wasn't there by an accurate estimate of the phase.  This location will be a rougher estimate in the presence of the other tone.  When you add a slanted signal (say a line) to a mode (a peak), it will shift the location of the peak somewhat.  Since you are interested in the higher frequency tone, the lower frequency one is going to look like a broad hill in comparison which is going to be less interfering than if you were doing it the other way around.
(I'm using the word "tone" broadly, meaning a pure sinusoidal signal.)