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Title says most of it!

My civic rattles like crazy with the Air conditioner on, out of gear,

I recently dropped the transmission for this problem, and it didn't get better. I can't seem to find anything on the internet linking the far end of the transmission to air conditioning... It sounds like the sound is coming from the very end bearing on the mainshaft.

Why would this bearing make such loud noise? and should it have been replaced when I had the transmission down? I replaced the end bearing that the snap ring goes into because it had a cracked race. and I replaced the input shaft bearing and seal.

All tests done with AC on. With AC off, all seems normal, goes through all the gears.

Out of gear, Clutch out, No Noise
Out of gear, Clutch In, No Noise
In gear, Clutch in, No Noise
In gear, Clutch out, Loud Noise

With the AC off, this same noise can also be heard during a "lugging" condition, (Not enough RPM and slipping the clutch (this is up on jack stands so the wheels are turning in the air. I haven't taken it down to test drive it yet. I'd like to hear some thoughts first.

 
Rep Power: 118

This is a little confusing, who worked on the inside of the transmission?

The “harmonics” due change when the engine is loaded by the Ac system, you already mentioned a bearing race failure maybe that was just a symptom of a collision that has tweaked the transmission case.

Audibly, something is still moving around in there more than it should.

 
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I worked on the inside of the transmission. I followed the book, I paid attention, It seems right, I put it on the ground and drove it around some.

The clutch goes all the way to the floor to make it disengage. But it does indeed disengage. The air conditioning noise seems to have went away so maybe the new bearing wore in? It gets through all the gears smoothly, So I believe it could be that big bearing at the end of the main shaft. That one wasn't replaced.

More concerned about the clutch and the wheels squeeking when turning. I know the alignment is off, Gonna straighten that up and drive around some more and see what it does.

 
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Drove it a bit. The transmission seems fine
Straightened up the steering and it's much better than it was.
I cant hear the noise with the car going down the road. Or when idling in a drive through like I used to. 😄 So maybe it finally lubricated?

 
Rep Power: 222

i had the bracket at the bottom of my exhaust manifold break clean in two which made a crazy rattling noise at idle, usually when the fans kicked on, didn't realize the bracket was broken until i pulled the manifold off to weld the crack that developed in it. welded the bracket back together at the same time

 
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The heat shield of the cat? Manifold heat shield?
I'm gonna check that out as soon as I get it back up on stands. I'll be a handful of hours.

Thanks for your input! I'm taking all suggestions.
Starting to wonder if it's inside the engine?

 
Rep Power: 222

No there's a bracket at the bottom of the manifold that bolts to the block. The rattling was driving me nuts because it sounded like a heat shield but way worse. Definitely check your heat shields though

 
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So here is something that I've noticed but forgot to mention, The Clutch pedal goes to the floor, but has resistance the whole way, but to disengage it completely, it has to be pressed all the way to the floor, before it would disengage completely after about a half of a press. It's a new clutch, pressure plate, flywheel, and friction disk, pilot bearing, input shaft bearing and seal, and countershaft bearing.

I bled the clutch twice, just in case I didn't get all the air out, I'm positive all the air is out.
The slave cylinder moves instantly when a partner pushes on the pedal.
It does completely let go when it's fully pressed, and fully engages after just an inch from the floor. The rest is just spring.

Any thoughts would be appreciated. I'm scared I didn't get something right. But I've never driven on "new parts" before so I don't know what it's supposed to feel like. haha.