That knock sure sounds like a rod bearing to me. Could be a wrist pin but it's more likely the shop did not check the bearing clearances with plastigauge.
I've had rod knocks in engines that only occur at particular RPM ranges. In the cases I've investigated I found the rod journal to be egg shaped. In other words if you put a caliper on the journal or plastigauge it on the less worn sides and then it may appear to be OK but you need to measure the journal for egg shaped out of round and left to right.
There should be no clunk sound when you rotate the engine by hand as you mentioned.
I'd pull the plugs and rotate the engine by hand again to see if you can repeat that clunk. It may give you another clue as to what is wrong.
Do you know if they used Honda rod bearings or aftermarket rod bearings?
To get the rod clearances perfect on these Honda engines, you have to look at the stamped codes off the rods and crank and get specially sized/color coded bearings to fit nice and tight. I rebuilt an 87 Civic 1.3 liter engine that I picked up from the junkyard. When I was putting it back together, I noticed that the aftermarket rod bearings were a little bit too loose, but still within the service limit so I went ahead and used them to save money. I used mostly aftermarket main bearings, but there were two that were too loose when I plastigauged them so I had to get the special color coded ones from Honda. BTW- the machinist that inspected/measured my crankshaft said it was not worn and the original bearings were in pretty good shape.
Yes, I agree 100% with Erik. When I replace bearings on a Honda I use only the correct size of bearing based on the color and letter/number stamp (rod and main bearings are coded differently and it's been a while). As far as I know only replacement Honda bearings use this scheme. If you use the "standard" aftermarket bearings you may get one that is loose or possibly too tight. Since they only come in one size.
If you don't know what the originals were you can calculate it and I think there's a table in the honda manual of measurements and colors.
The other possibility is what happened to me once. I plastigauged the rods and main bearings. All was within spec. Then took it all apart to clean off the plastigauge and oil the journals before tightening the caps down to spec.
After assembling the engine I was turning it over by hand and noticed a very slight clunk. I pulled the pan off and by grabbing each rod bearing and wiggling I found the loose one and that a spec of something had gotten between the mating surfaces of the bearing cap and rod. Cleaned it up and all was well.
Yeah well, if you dont watch out, free time can cause more kids! Anyway, I tried the coast down method in 5th and the oil light never came on but just before the point of stall I can hear the rhythmic knock. Its looking more and more like a tear down every day. I was afraid of damaging the pressure plate springs because I read on there website that lugging can do that.
I still need to feel the clutch for and spin the engine over by hand with the spark plugs out.
I can't imagine how low RPM or lugging could damage, of all things, pressure plate springs. I don't suppose you have a link to that? I'd love to read the explanation, there could be something for me to learn.
Ah. That's not the pressure plate, that's the clutch disc. The springs in question, named "torsion damper" in that document (I've always wondered what they're called), take up excess torque gradually to reduce shock to your drivetrain and engine when you dump the clutch too harshly.
For those springs to fail from high torque makes sense, although I doubt low RPM is required.
Cool file, I'm going to read the rest of it. Thank you!