Mine runs really rough, and got the CEL. The cods probably had been there a while but I didn't check until I got the CEL. Mine had the clicking as well, which went away after the valve adjustment.

 

So I replaced the sparkplugs with factory spec NGKs, the car actually ran perfectly smoothly for about one minute, maybe two, but then started running rough again and the CEL came back on, though it's no longer flashing. It's still better than before, but not totally resolved.
I bought a multimeter tool to follow the procedure in the factory shop manual for checking the individual coils and will let you know what I find there.

 

Turns out all I needed was to replace coil pack on cylinder number two. Runs like new now. It turns out the Autozone branded coils are actually manufactured by Denso.

 

So I tried both #5 and #7 out of the 8 OP posted above. My MY01 had a misfiring issue last week and I I checked my spark plugs and replaced them with the NGK spark plugs that was recommended for the vehicle. I found out that there was one bent spark plug. So after swapping out the spark plugs the car drove like new. However, over mothers day weekend I started my car again and this time the car was misfiring again and I could hear some popping noise from my exhaust. The car sounded like crap! My car sounded like a damn subaru and so I'm thinking it's probably a coil pack problem and after doing some research on the forum I decided to swap my ap1 coil packs with the 04-05 onces. So after swapping it out the car sounded a little bit better but it still sounds like shit lol. I'm hoping it is nothing serious like a bent valve or having to swap out the ecu. Hopefully it's something minor like a valve adjustment problem. I just got myself a engine code reader so ill try to keep an update.
I took some videos maybe someone can help me out if they know something that I don't.

[media]https://www.youtube.com/watch?v=8WmGEmTq8J8[/media]

 

So I ended up buying an engine code reader. The codes that the reader pulled up was p0300, 303, 304, and 1399. So I ended up checking the spark plugs on cylinder 3 and 4. I can tell they didn't get any sparks so i'm guessing it might be from a blown fuse or something wrong with the ground. I'm gonna take my car to the shop tomorrow to get a much need valve adjustment done but I hope all is resolved by tomorrow.

 

I figured out my problem it was a bent valve. I had a feeling oh well I guess a new head will do.

 

i did a compression test
245
245
255
255

bad?

 

I "used" to love my s2000... every time when I pump gas... I would not close it all the way (until there's a click)... I used to get missed fire... until one day i decided to closed all the way until there is a click... my missed-fired is gone.. sometime it's not good to love your s2000... LOL... (sorry if someone already posted this... it's 8 pages of reading....)

 

good.