Note that samplers usually introduce a bias (shift of the zero-point crossing), and depending on how well you have grounded both computers, hum. Normal cables act as antennas, picking up interference from electronic equipment to varying degree. Make sure you connect sound only to line-out/line-in jacks, not amplified outputs or mic inputs, or you will get distortion. USB sound cards for musicians are usually the best (least likely to pick up electronic interference on recording/playback) for the PC, and AMAS is a good sampler for Amiga (bit cumbersome software though, but it samples stereo if you need it.) Combine stereo to mono by software/settings in the PC before sampling, ie. don't plug a stereo 3.5mm plug in a sampler's mono 3.5mm hole.
GoldWave can load/save Amiga IFF and reads raw, just input frequency, 8-bit signed PCM mono and it loads correctly. Raw can be had by saving as IFF and re-save the sample in Protracker or Audiomaster, or by saving as raw and specifying PCM 8-bit signed mono.
When converting from 16-bit to 8-bit, you *will* get noise and distortion on low volumes (such as faded out ends of instruments), simply due to aliasing. Going from 11kHz to 28.8kHz improves this, but only slightly. I've planned and am about to code an improved converter, but I'll give sox a go - if it's better than GoldWave/Soundforge/Wavelab, I might save myself some time