No, a few second difference will not affect how the boots mold.
Most people have slightly different sized feet and that is likely what you are feeling. Personally, my left foot is about 1/4 to 1/3 of a size larger than my right foot. If I size boots to my right foot, the left feels tight, and if I size to my larger left foot, my right get a bit of heel lift.
What I usually do (with burton boots) is size to my larger left foot, then get some J-bars to lock my right heel in. That's not your issue though...
I would NOT heat them up again. I rarely tell anyone to actually use heat to mold their boots, as the heat from a couple riding sessions will do it for you. If you try to re-heat mold them you could end up breaking in more than you want to in other areas, like the heel for instance.
I would just throw on some thick socks, or two pairs, and then tighten the lower section of the boot as much as possible. Don't even wear normal knee socks, as you are happy with the fit around the ankle and calf. Wear 2 or 3 pairs of ankle socks. Tighten the boot up and seriously go jog around for awhile. Just deal with the pain and numbness for as long as possible now while running around the house, and when you actually take them riding with a normal thickness sock it should be much better. I have numerous friends that will wear their new boots around their work for a day, just to break them in slow and proper.