loud rattle clunking noise!!! plz help

mp51987

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mazda protege5 swagon
Ok so i recently put a new motor in my 02 protege5 the old motor had 245k miles and blew up on me. I got the new motor from aplace called LKQ idk if anyone knows what that is but its a used parts place that distributes all over the US. Anyways i put the motor in around three weeks ago. For the first two weeks it was running perfect. Then one day at a stop light i noticed a weird loud rattle noise. The noise changes when you push in and let out of the clutch. In my times with civic that usually means something to do with the transmission. Well i stopped at a shop and he just listened and took for a test drive and says its the bottom end. When driving it for a while it seems to go away a little. But atfirst when u start driving it, when shifting up and pushing in on the clutch u hear something spinning. Does anyone have amy ideas.or thoughts? Im thinking throw out bearing, inputshaft, input shaft bearing, or maybe pressure plate. Plz dig deep and maybe help me out.
 
It doesnt stop when the is pushed in it just gets a lot quieter. Figured id throw this in to.
 
The sound happens in neutral. When you push in the clutch it gets a little less. But u can still hear it a little. Its not a steady tick tick tick tick its more of a rattling noise.
 
Yes it gets lowder when in neutral lol. And im thinking its the motor now. For some reason the cel will start flashing as soon as u start the car now. Idk what to do.
 

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