I have an 89 SI 4WS B20A. It had been sitting for 2 years with a new engine replacements and transmission replacement from Japan. It had been running great until recently after I finally fired it up to drive. I noticed the speedometer will work and then stop working and my S3 light will flash and then a check engine light will come on. Then all of a sudden the speedometer will start working again as normal. The odometer never stops working. The other issue is at times after it seems to warm up it will idle rough and then if I press on the accelerator to get the RPMs up it will smooth out this doesn't happen all of the time. Sometimes it's really bad at a take off but other times it's perfectly smooth. I notice it will also run rough when the fan comes on at times but seems to run smooth when it's cool for a few minutes. The running rough just started. A week or so ago. I just started driving it again about a month ago. At first it acted like a slight misfire. Now its worse. All new plugs, cap, rotor, wires when rebuild was done. I recently put a new cat converter on it and its OE spec. It was only driven about 2000 miles before I parked it. The speedo cable is new also. It ran perfectly fine before I parked it also. Any ideas?

Is that check engine light still on? Just make sure both those cams are on perfectly. Many problems with that.Does sound like ignition so far. Hows the fuel filter?