Does it continue to miss, or does it smooth out later? Also, does it set off any check engine codes?
An engine will heat up a bit after you shut it down, and electrical devices that are on the brink of failure might misbehave as a result. If this is a distributorless engine, I would look at one of the spark coils. My stepson's 93 also had a problem that appeared when it got hot (usually after being parked, but also occasionally while running) which turned out to be a bad splice in the wiring harness, which increased its resistance just enough to kill one of the injectors. This problem sent a trouble code - an unhelpful one, but something.
I think your first job will be to see if you can narrow it down to fuel or spark. A vacuum gauge would be very helpful there.