One thought: does it do it in all weather?

If it's more in damp conditions it would point more to being an ignition wire problem. That might trigger the random misfire code. I had an Accord that behaved exactly as you describe in damp cold weather. You could test that theory by spraying (soaking) the ignition parts & wires with WD-40 after you experience the symptoms, then drive it again. New wires fixed me right up.

But if the computer says you have a vacuum problem (via the code), then you probably do.