The port in the S38 is flared differently, when u feel down the inside of the port in the original it tapers down while the S38ii has a more straight through feel. If I recall they were using a bose patented design and had to change it in their new design.
The cosmetics are changed and the dimensions slightly.
There's a bigger grill protecting the tweeter on the new model and the surround on the midrange is rubber. I think the cone composition is different on the midrange but the sound is still the same. I actually think the midrange surround on the new model is slightly smaller than the old model.
Sound statistics are supposedly idenital though there are probably slight differences due to the minor changes. I've A/B tested both S38s and found the S38ii to be significantly worse though they weren't broken in yet.
Just the port, not the rest of the speaker. The JBL Studio series and Bose are very very different speakers. No tiny cubes or direct reflecting crap is in the Studio or Northridge series.
I have Series I S38 (did a direct comparison to the PSB Image 2B and choose the S38), and Series II S-Center and S26. I checked out the 4" driver on the center and s38, they are a different material (the S-Center 4" surround now uses the same material as the 8" driver). But the surround is still the same size.