First off, do you understand what creates pops or clipping? Once you understand that, it's easy.
Secondly, I believe there is a secret registry function in FamiTracker v4+ that makes N163 less noisier. Which brings me to the question, are you talking about FamiTracker or NSF exports?
Well, I have little luck with looping sample beyond simple sound waves. So, lets get to a example of 8 samples long wave. Five of them complets one single wav(40 samples long). How should I number them in wave settings? Like this: 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4? To your second question, right now I'm only focused on Famitracker.
Just upload an example ftm. Best way to help is to be able to see exactly what the problem is. With you just explaining, it is vague and I am not sure how to help.
Oh I guess you're trying to use longer waves by connecting multiple ones? That's not really going to work since 60Hz (or 50 in PAL) is way too slow for changing the wave just as it completes one cycle.
