Actually, I believe that the 5/3/1 and 5/3/1 Reloaded articles both call for 5x10-15 on the assistance work. i.e Workout 4 in the "Triumvirate" template in the 5/3/1 article calls for 5/3/1 Squats, 5x15 Good Leg-presses, 5x10 Leg-curls. However, I don't know if Wendler writes it up differently in the manual than in the articles.
OP - Proper warm-up/cool-down, peri-workout nutrition hot/cold contrast showers PWO, daily foam rolling, stretching, mobility and active recovery stuff can all help reduce muscle pain. However they are also pretty boring, so most people don't do them consistently until they have to. Some soreness (DOMS etc) is normal and can be managed. However if your main lifts are legitimately suffering, then you should probably back off a little on the assistance work. Of course, if you're suffering to make your main lifts, well that's perfectly normal. Adaptation takes time and it's inevitable to struggle from time to time.
More info regarding how long you've been training in general and training 5/3/1 specifically, as well as your goals, nutrition and what exactly is happening in your workouts when your main lift is being "affected" (i.e. are you missing lifts or does it just really suck etc) will probably get you better advice. Just my $.02
All the best.