You mentioned a reluctance to switch from Cy3 to Cy5 because of results with
various secondaries. Cy5, though not very bright to the eye, is quite bright
to CCD devices and should have very little bleed over into FITC channel. Also
the idea behind having a series of cyanine derivatives was to permit exactly
what you're concerned about, to freely move to other wavelengths without
having to worry about the behavior of a different fluorochrome/probe
conjugate. The cyanine fluors do have differences between them but not to the
extent that switching from say FITC to Texas Red would produce. I would think
you should be able to move to the Cy5 conjugate with very little modification
to your technique.