If anyone has any advice on how I could possibly improve the sample quality or anything, feel free to advise.
You can sample them in 16 bits instead of 8 on your peecee, at a higher sample rate, and sample each instrument in multiple octaves (just make sure you can still use that sample rate on Amigas).
Need 8 bit? Maximize their volume and convert to 8 bit (make sure the samples don't clip). Also, don't let the instruments fade, use music software to do that (Amiga hardware volume settings are MUCH better for 8 bit fading).