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Hey guys, been lurking around here for the past few years and have found some great information from here!

Now I recently replaced my transmission with a used JDM Transmission with "low mileage 30k-60k" supposedly a SLW code transmission.
(old trans wore out from consistently low trans fluid, I swear I replaced every seal in the old girl but couldn't find the leak lol)

I installed a fresh clutch kit (exedy) and flywheel along with the bran-used transmission. Install went okay with no issues to report, surprisingly easy to swap out the top and leave the engine in the bay.

Now I'm getting 2 noises within these first 400 miles(all kept below 3k rpms, except for a few tests regarding rpms for these noises)

1. Unusual grinding/humming noise in any gear when clutch pedal is in the released position(N,1,2,3,4,5) The noise increases with rpms and I haven't found a gear nor rpm where noise isn't present. I have narrowed it down 100% to the transmission using my hand dandy long screwdriver. Sound almost like a bearing noise. I'm not entirely sure which bearing is making said noise though. I'm looking at possibly a pilot bearing or ISB.
MTF level is good so I'm almost sure it is not related to a low fluid level.

You guys have any idea which is most likely? I'll attempt to post a link to a video with the noise if I can get it uploaded to Youtube.

2. When releasing the clutch pedal at low rpms, I'm getting a clicking/clunking/popping sound in multiple clutch positions. The sound happens in all stages of clutch engagement. I suspect possibly the greasing of the input shaft? I greased the splines, the clutch fork mushroom bolt, where the fork contacts the throwout bearing, and the end nub that goes into the pilot bearing to help with transmission seating. I'm concerned that I should have greased where the bearing glides on the input shaft and that it is possibly binding there. Should I have?
Both CV Axles seated perfectly when reinstalled.

I appreciate any and all information or ideas you guys have for me, I don't have many in person sources of reliable information about these kinds of issues.

Thanks,

Nate

 
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I am curious , when you reinstalled the transmission was there a splash shield behind the flywheel. The reason why I asked this question is because I am in the process of doing a clutch job. I noticed the splash shield on my transmission had some scarring from hitting the flywheel at some point in time. I did a post on this question but so far it has not showed up. I'm thinking about leaving this shield out and making something on the outside to protect the flywheel. Anyway, I hope you find the problem.

 
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There should be a splash shield for the flywheel, held in by 2 m6 bolts
on my EX there is also 2 "Stiffeners" bolted to the oil pan and transmission casing
you could possibly straighten out the splash shield with a hammer and some wood as an anvil, hit her with some black paint and she should be good as new

HOWEVER, if your flywheel is in anyway hitting that shield there's a problem! Could be more than just a splash shield issue. I would investigate more into it to be sure.

I'm sure people will get to your post but please keep this thread on topic from now on. If you have any more questions please DM me.