I've looked over the internet and haven't been able to find a comprehensive list of version differences, like there are for other games like Zelda 3 and OoT. As someone considering running this game, I have two questions about regions:
A: Aside from language, what are all of the differences between USA and JPN?
B: How much time does JPN save over USA?

I think the major difference is how Tower of Spirits 6 is, it is basically shorter in JP than US/PAL (idk about PAL, this is a guess)

I do know that Spirit Tower is Faster On JP

ToS6 is the big change with a floor being skipped in JP iirc. There's also a slight change to ToS5 in the floor design. Screenshotted from Indy's and Poke's runs, but you can see the difference on the map. Generally easier on JP.
https://imgur.com/a/Tydsa

So Tower of Spirits 5 & 6 are the only gameplay differences? Is it known how much time is saved with these gameplay differences along with the text boxes?

This save around 5-6 minutes

The final floor in Tower of Spirits 6 on English has become optional on Japanese. This floor by itself took 2:30 roughly.
The start of Tower of Spirit 5 in Japanese no longer supplies a bomb pod. This does not slow down gameplay, but makes the start of this section a lot harder.
Arrows de-load when off screen, making this shot on English impossible to do on Japanese. The room layout in Japanese also is slightly different.
The screenshot that Scarlet provided is also another change in Tower of Spirits 5. This one I believe was around 40ish seconds faster.
The text technically is faster in some places when you can't instantly scroll the dialogue, but I myself haven't timed it.