Atmospheric line-of-sight (LOS) wind measurement by means of incoherent Cabannes- Mie lidar with three frequency analyzers, two double-edge Fabry-Perot interferometers, one at 1064 nm (IR-FPI) and another at 355 nm (UV-FPI), as well as an iodine vapor filter (IVF) at 532 nm, utilizing either a single absorption edge, single edge (se-IVF), or both absorption edges, double edge (de-IVF), was considered in a companion paper [Appl. Opt. 46, 4434 (2007)], assuming known atmospheric temperature and aerosol mixing ratio, Rb. The effects of temperature and aerosol variations on the uncertainty of LOS wind measurements are investigated and it is found that while the effect of temperature variation is small, the variation in R(b) can cause significant errors in wind measurements with IVF systems. Thus the means to incorporate a credible determination of R(b) into the wind measurement are presented as well as an assessment of the impact on wind measurement uncertainty. Unlike with IVF methods, researchers can take advantage of design flexibility with FPI methods to desensitize either molecular scattering for IR-FPI or aerosol scattering for UV-FPI. The additional wind measurement uncertainty caused by R(b) variation with FPI methods is thus negligible for these configurations. Assuming 100,000 photons from Cabannes scattering, and accounting for the Rb measurement incorporated into the IVF method in this paper, it is found that the lowest wind uncertainty at low wind speeds in aerosol-free air is still with UV-FPI, ~32% lower than with de-IVF. For 0.05<R(b)<0.07, the LOS wind uncertainty is lowest with de-IVF, and for R(b)>0.07, the IR-FPI outperforms all other methods. In addition to LOS wind uncertainty comparison under high wind speed conditions, the need of an appropriate and readily available narrowband filter for operating the wind lidar at visible wavelengths under sunlit condition is discussed; with such a filter the degradation of LOS wind measurement attributable to clear sky background is estimated to be 5% or less for practical lidar systems.