Crank position sensor I might say, maybe, in some cases with oil leaks and such, dirt and such could build up on mag pickup and create issues, but you low mileage discounts that, but the intermittent nature of the misfires leads me to a break in a wire somewhere... And that sucks! You'll have to check the wiring harness.
Have a 2001 SE and had similar problems but to another extent where the engine would stumble, always kept up on maintenance so didn't run through the litany of replacing all you have shown here. Car would run great but then next time, it would almost stall at a light, etc. When I hit the proverbial brick wall when tracking things down, so I took it to a buddy. He uses some diagnostic system (for mechanical shops) that he pays for and they have a database that tells you probability of problem based on diagnosis. It said a short in wiring loom by AC condenser. So Lo&behold, once it was opened up there were two wires that were kinda melted from sitting on the condenser, think they were from the crank circuit. Fixed that and never had the issue resurface.
You may very well have the same issue but the low mileage may not have compromised the wiring as much as mine had been. Think my SE was at 180k then and today is still running very well at 265+k.
Check out that spot... And if you get tired of that SE with 50+k on it, drop me a line ; )
