Pasta – the difference between 100% whole wheat pasta and 100% whole wheat couscous

It sounds like it might have been fregola, a toasted pasta from Sardinia. It is quite similar to Israeli couscous. There is nothing wrong with the cooking technique you are using, I think you just might have found a brand/batch that isn't very well made. If there is a lot of unevenness in the toasting or size of the pieces, then that will likely result in an uneven cooking in the liquid. As you can imagine, the darkly toasted pieces have more of a shell that makes it slower for them to absorb water. Don't give up on fregola though, it can be delicious stuff. You can also buy regular Israeli couscous and dry-toast it in the pan for awhile before adding the other ingredients.

00 is extra-fine flour, the most refined grade. Here's a useful page for more about the old flour grading system. Other than pasta I use it for thickening sauces, and I sometimes make pizza dough with it, although I can't tell the difference between using 00 and good quality bread flour. I'd use 00 for Gnocci certainly as the chefs do, but most home cooks just use plain flour and seem to get good results.

Basically, if you have it or can get it use it, if not plain flour is fine.