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The Honda Mechanics Manual says each cylinder should be between 10% of each other, which these meet the criteria.
6) I checked the timing with a timing light AND a OBDII computer reader to check the timing that both confirms it is in the range of 6-10 degrees, which according to the Mechanics manual for the 2004 Civic its 8 degrees + or - 2 degrees, so that seems ok.
Here is a dumb video I made, but it will show the engine:
Another thing to check is make sure you have the correct drivers' side mount. I had this same problem once where the wrong mount was given and it looks similar. The sedan and coupe mount are different and some part stores do not discriminate . Here is a link of a thread a few down on this page covering this.
Have you noticed any difference with the A/C on or off? I had my A/C recharged at 105k. HUGE rises and drops in RPM, even at a stop. Turns out my compressor was going out. I confirmed they put in the right pressure, but the compressor couldn't handle it anymore. They decreased it to where I could live with it till payday. Had the compressor worked on, refilled to correct pressure, and the little RPM dance stopped. They had also told me that if it didn't fix the issue, it could be a leak in the manifold.
Any of the pros feel free to confirm/deny this. Just relaying what I was told.