After converting, you might want to reduce stereo separation. The extreme separation used by 4-channel mods on the Amiga can sound quite bad with headphones. I suppose most sample editors should be able to compress the stereo image. Some players also incorporate this feature. At least EaglePlayer on the Amiga can mix the channels, although I don't think it has a diskwriter feature. I know XMP and UADE on Linux can do this.
Normalizing the volumes might also be desirable.
On Windows, SurfSmurf's Oldskool plugin for WinAMP has generally been considered the most accurate player for mods. WinAMP can of course write to disk as well.
