Hi @slh277,
In the original comment I made about the 120 bp quality drop-off point, I just assumed if you were to truncate your reverse reads at that point then there wouldn't be enough overlap to actually merge the paired ends. That's why I originally mentioned that perhaps the forward reads alone be adequate, especially since they seem to be very good in quality. In hindsight I made that comment without taking into consideration your targeted region and primer sets.
I guess the point to emphasize would have been to ensure that following your trimming choices, there be enough overlap to properly join them. See this comment regarding the required overlap for DADA2. That being said, I am however curious how extending your reverse read trunc parameter to 200 (as was suggested above) affects the outcome, so if you could report back on that, that would be very appreciated and would help with my own truncating decisions in the future as well. 