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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. 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 always worked fine before I parked it also. Any ideas?
 

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My speedo was acting strange, bouncing, stop working, work, bounce (by bounce I mean within 3 to 5mph it would bounce). I fixed mine by taking the top side of the speedo cable out from the sleeve and lubing it according to: http://www.prelude3g.com/p3g/frameset.htm - Speedo can cause CEL when its not working properly due to the cruise control system reading from it.

My 89 also has the weird shakyness when the electrical system is under strain. Theres a host of reasons that may be. From my research (im a noob ive only owned my lude for about 4 months), the IACV has some impact on it, so maybe a cleaning/replacement/test of the IACV according to the service manual would be in order. Potentially your alt/voltage regulator may be at fault.

Basically if i have the lights/fans/blower going my RPM would drop to the rough shaky rpm, Until i diagnosed the problem, I just increased my warm idle to 1000rpm and that got me along just fine (would just cause the car to idle under electrical load at its "normal" rpm, and idle "high" under low/no electrical load, until i cleaned up the IACV which the screen was completely carboned and full of junk. Then I returned the idle back to normal.

I hope my words are of some help for you.
 

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Speedometer issue first. The simple fact that since your odometer is still working when you speedometer isn't tells me that the cable is still working. Now, there are varying degrees of "not working". When it's not working, does the speedo read 0? Does it freeze in position? Does it just bounce around? How long does the speedometer malfunction last? When it's not working and the odometer is, is the odometer still giving accurate distance readings? There is a vss (vehicle speed sensor) on 3rd gen Preludes. On the 88/89 models part of the gauge cluster. On 90/91 models it's mounted to the transmission. I suspect the vss is going out on your car, but more troubleshooting is needed.

As far as the engine issues go, I have one question...have you read the trouble codes from the ECU? You said it throws a CEL, which means it has stored trouble codes. Read the trouble codes before doing anything else to fix your hesitation issues. We can tell you how to do that, and what the codes mean if you don't know.
 
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