Well, I bit the bullet and bought two Seymour-Duncan Apollo Jazz Bass pickups top replace the stock pickups in the Stu Hamm Standard.. They are humbucking. The bass is totally quiet now. The width and height fit perfectly, but the depth was bit deeper than the originals. I put them in without the back padding, but they are about 1/8" too far from the strings. If I use the supplied rubber backing, I will have to cut them in half lengthwise, because if I used the whole pad, they would be too high. For the moment, they are working great, and I will leave well enough alone. Looking forward to recording with it soon.
I usually prefer the tone of pickups that are not too close to the strings, it seems like the overall response is more even and the attack is smoother.
If you don't have any hum or gain issues then maybe they are in a good spot. You can try raising them, in particular the bridge pickup so it balances better with the neck pickup.