Yup. Differences in the ejector, extractor, recoil spring in addition to the barrel and magazine. Like DWalt said, best approach is to set up an upper (slide, barrel, recoil spring) for use with .38 Super, and you will still have to R&R the extractor in your lower each time you swap back and forth.

Another possible issue will be the barrel link, which locks the barrel in battery to the slide (these are made in several overall lengths to allow fine tuning of that critical function). After setting up the new barrel with the barrel link I would peen the link pin firmly in place and keep that together as a unit.

I would wait until the barrel arrives and slug it for groove diameter, then choose bullets accordingly. My old Colt Super .38 handles just about anything, including cast .357 SWC up to 150 grains, but I'm sure most will do best with 9mm bullets in the usual range (115-130 grains).