I'm doing the original 5/3/1 and also squat mondays, bench wednesdays, press/deadlift on Friday. On Tuesdays and Thursdays I'll push my prowler.
I sometimes deviate and squat on Sunday or move things around as needed depending on what my upcoming week (workwise) has in it.
If you are going to condition after squats or what have you, ease into it and slowly add the volume. I started with an empty sled, moved on to the prowler challenge, and have recently worked up to 230 lbs on the prowler for 6 trips on my conditioning days.
Most hardgainers just don't eat enough. If you drink protein drinks, add olive oil to them. If you use light tasting oil, you won't taste it. An easy way to add calories.