Hi guys, I've always lurked around the forums and learned a lot from the time I picked up my S2000 a few months back in February.

I bought the car (MY00) with 113k miles on it from South Carolina. I thought the body was nice with no rust. I'm from Massachusetts, so no rust is a plus.

After buying the car and driving about 100 miles the check engine light turned on. I didn't think too much of it because I thought the car still drove normally. I finally got home after a couple thousand miles and finally pulled the codes. I probably should've done this way sooner. I was getting P1399, P0300, P0301, P0302, P0303 and P0304. The car is catless with a Single exit exhaust.

So I proceeded with a tune up:
-Fresh fluids
-changed plugs to OEM plugs
-ordered some Denso coil packs off of ebay (I didn't trust then; stupid of me to buy them at the $50 for 4 price). Later I bought original Denso coilpacks off of Rockauto.

Reset the ECU and it was still missing on a couple cylinders. Did a Compression and leak down test. Those came back bad with low compression on Cyl 1, 2 and 3.

I then contacted InlinePro in Virginia and shipped out my long block to be rebuilt with 10:1 compression, forged rods and pistons. I plan on boosting. InlinePro did the valve adjustment and the whole motor was gone over. I didn't test for compression, but I would think a new motor would be good. I used a new intake manifold gasket while installing the intake manifold. The motor came back and I installed a new clutch since I had the Trans off.

I installed the motor in the chassis with new motor mounts, cleaned the injectors with a 9V battery and carb cleaner.

Today: I'm still having random misfires on all cylinders, you can hear a pppa pppa pppa sound from the exhaust once in a while. I'm not sure what I can check/ do next. I'm considering sending the S to a mechanic, but I've came so far and the issue is still there.
Could it be the ECU?
Is it because it is catless?
I retaped the whole wiring harness when everything was in pieces and all the connectors seemed to be in good shape. Do I need a new harness?
Do I need a defouler for the Test pipe?
O2 sensor?

Hoping I can get some help from you guys!! Maybe I'm missing something obvious

 

There's a comprehensive misfire guide on here, have you taken a look at it yet?

It is located here/
What I looked at when I had a misfire, other than what you have done, is injectors, idle air control valve, cleaned the throttle body, and I also reset the ECU and did the idle learn procedure. These are all relatively easy to do, might as well try em!

 

I have looked at many misfire guides and scenarios on here. Usually I do reset the ECU after I try something different.

I did clean the throttle body and MAP sensor today. So far the car hasn't thrown the CEL. The car seemed to have liked those two things being cleaned because I haven't heard clear evidence of the pppa pppa sound out of the exhaust. It was driven about 20 miles. Hopefully that was it. I plan to drive it later and putting more miles on to continue breaking in the motor.

Max, I appreciate the link. I'm gonna continue to read up on more scenarios.

I'm gonna keep my fingers crossed

 

*Update*

I drove a little over 80 miles earlier and there's still no CEL. Seems to idle smoothly and steadily around 950-1050 rpm.

One thing I'm unsure of is when I drive over really bumpy sections of road it seems to jolt a little bit. I'm not sure if that's just my foot going on and off throttle, but I'll pay more attention next time.