I've noticed the stuttering has stopped on at least four separate occasions, each one being after a separate reload. I'm not sure what stopped it, but one time it just stopped after a while of me not doing anything, so either something I did earlier had an effect later, or the problem just fixed itself.
It seems there weren't any goblin ambushers around, but there were some goblin thieves (snatchers) and kobold thieves lurking around to the south of the fortress, in the area near the lava pool. Maybe they had something to do with the stuttering.
I tried some other things in addition to what I mentioned earlier, like uncluttering workshops, removing stockpiles, making extra stockpiles and creating an additional garbage dump to allow items marked for dumping to be chasmed. Most of these methods gave the impression of stopping the stuttering at one time or another, but I couldn't get any of these to reproduce reliably, so it was probably coincidence.
I have a feeling it was the lurkers by the lava pool, or wherever else they may have been. I tried hunting them down but couldn't usually seem to find them when I wanted to. Anyway, if you've played the fortress further in the meantime, I hope the stuttering's stopped. Let me know how it's going if you can.