but nothing seemed to be working properly
so comment outed a lot
and went into the debug mode

It looked fine to me, I listened to it and it sounded fine as well. Then, to make sure s1 was working properly I disconected everything but s1 from the DAC and listened to just s1. s1 does change it's pitch but it's very, very low. At times I couldn't hear it and needed to place my hand on the woofer to be sure it was playing as it was so low-pitched. In fact, I think many normal speakers would have a problem with playing sines of such a low frequency.

I think that's where your issue is; the tones are very low and likely hidden because of higher overtones. Perhaps you would like to try the "Blit" or a similar band-limited Ugen. With those you can controll the amount of harmonics in the wave so you can still have a very low tone but you'll have more controll to make sure it has at least a few audible harmonics.

Yours,
Kas.