You will not be able to perform the aerosol retrieval with no SWIR bands so you might try increasing the initial visibility value to 80 or 100 km. You should still be able to perform a water column retrieval using the 820nm band. Negative values over water are not uncommon and FLAASH isn't really intended for correcting images over water. You can still get some negative values over land, particularly in the shorter wavelength bands (blue-green). They tend to occur in shadows and water areas but they should not occur all over the land areas where there is vegetation and more reflective materials. Look at the overall spectra to see if the the majority of the land pixels look reasonable.