I had the same problem with a gap after installing a BAT kit on my car.
I ended up pulling everything apart. I used a shorter retaining nut on the strut, and I also replaced the upper strut mounts. No more gap and everything looks as it should.
To anybody replacing your struts/springs, spend a couple hundred more dollars and do a complete overhaul with new struts, springs, strut mounts, lower control arms, sway bar links, and bushings. Also think about replacing the inner and outer tie rods if your car is approaching the 100K mark.
It's a PITA to do the spring/strut job, but replacing a bunch of worn out suspension components doesn't require a whole lot more work. You'll be rewarded with a car that feels better than new and all set for another 100K.