Thanks for your really helpful tutorial. One issue I had running it with my own data was doing cutadapt in one step as it didn't trim the adapters correctly. Running it in two steps seems to work though. I think there have been a few other reports of this on the forum.
In case you're interested in the original issue and solutions: ITS cutadapt trimming of primer and reverse complement of the reverse primer and cutadapt / trim-paired / option "front" and "adapter" and Cut-adapt trim paired - different results when primers separate vs linked.