I got the boom arm in yesterday, so I was finally able to assemble everything.
First, the base portion is very loose on my controller. I had to get some paper and fold it multiple times to stick on the underside of the controller to beef it up to make the base snug.
Second, the thumb screw I had (generic from a PC) is either too thin or not long enough to go through the hole for securing to the controller. I had to improvise and use some random screw I had in the garage.
Thirdly, as gilrad has mentioned, the base that the phone sits on impedes on your pressing triangle or up pretty easily. I'll definitely need to dremel off some portion of it to make that area a little easier to access.
After all of that, I enjoyed the hell out of it last night. Played through Megaman 2, River City Ransom EX, and some Altered Beast.
Pro tip: In Nesoid, Snesoid, Gensoid; go to Other Settings, Shortcut Keys, map quick load to L2 and quick save to R2. Nice for getting to the save states readily.