So, I rode three more times yesterday to see how it compared to my first run. Everything seemed the same, although some fog effects didn't go off on my middle run.
Yes, the dark ride scenes are slower. It is extremely noticeable to those of us who have ridden this ride a thousand times, BUT, it does mean no more sound leaking from other cars between scenes, AND creates a pretty cool dark ride feel for the beginning that sets expectations for a relaxing slow-moving dark ride better than it used to.
The launch feels exactly the same as it used to.
The coaster segments feel exactly the same as they used to (since they use gravity, not sure they have a choice anyway).
The little drop after the fake out ending feels smoother, so definitely feel like if any track was replaced, it was that section where the multiple fog blasts hit you.
Sounds aren't as noticeable for the fire ceiling, and we now start rolling into that last drop a little early. I like the subtle roll into the drop, feels neat. Feel like we need a sound cue to notice the fire ceiling better, but then again, maybe it's fine and that's just me.
So anyway, after riding several times now, the ride, when it is working, is I think working as intended to. Tire drive moments are slightly slower for dark ride scenes. But that really only affects the first few scenes.
EDIT: Oh, and all the strobing flats along the coaster segments lit up perfectly for me each run, so that one time they didn't was probably an error, maybe from the mistimed launch as theorized.