Microsoft One Note and Evernote are great for storing all your shit and adding web clips and photos. One note I think you can even sketch in it.
Penultimate is a really good app for free form note taking with finger or stylus. It will do handwriting to text and it is a part of the Evernote system so you can quickly add your handwritten notes to n Evernote notebook for each specific project. It also records audio so you could narrate as you walk a site.
Evernote and penultimate together do pretty much everything you want. And on an iPad pro with the apple pencil it works like a charm. I still haven't found another stylus that works very well without delays, inaccuracies.

If pencil comes to smaller iPads I think that would be a great solution. The pro is kind of unwieldy for walking a site.