5/3/1 I just use as the protocol for my main lifts. That is where it stops I feel. The remainder of my workout, the 'assistance' exercises, I use to manipulate the overall volume. I need more volume than just 2 or 3 assistance exercises, so I use anywhere from 4 to 8 depending on what the days focus is. I.e. bench = chest, deads = back, military press = shoulders, etc.
I tried one of Wendler's sample programs. I liked it a lot, but I didn't feel it was enough volume on the assistance work to get what I want out of it.
Basically if you feel like you aren't getting the most out of the sample workout, then make adjustments where you feel there need to be adjustments. If it's right or wrong, that doesn't matter. It is a learning experience and you'll determine what works better.