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I have a 2004 DX Coupe with the 1.7l and a manual transmission with 104k miles. Last May ('23) I had a throw-out bearing go out on me mid drive and I had to clutchless shift on the way home. Apparently, the throw-out wasn't completely disengaged, because when I had a shop put in a new clutch, a bushing on the output shaft was ground down and wouldn't hold the new bearing properly. As a result, I purchased a JDM transmission for $450 and they put that in. I haven't had issues since then.

However, yesterday I suddenly was unable to keep the trans in second gear. It would pop out when letting out the clutch. There was no grinding when going into gear, and no grinding when popping out, just won't stay in 2nd. 1, 3, 4, 5, R all work fine. Now, I can over rev 1st gear and shift to 2nd, holding it in gear while I let the clutch out. Then I hold it in gear while I accelerate until ready to shift to 3rd. This only works when accelerating. I cannot get it to work downshifting or going slowly, just grinds. Obviously not a sustainable way to drive.

I have read a few other threads about a similar issue. Typically, they go like this: engine/trans mount replacement fixed the issue, fluid change fixed the issue, loose/bent gear shift linkage replacement fixed the issue, or trans rebuild fixed the issue. The kicker is this; JDM transmissions have supposedly a max of 100k KM on them so internal issues doesn't seem likely, the shop that installed it should've put new fluid in, so I don't suspect that issue, I recently had a state inspection and they only flagged one motor mount which I already replaced. That leaves a loose or bent shift linkage. This may be the case since 2nd gear is the furthest from the transmission (2nd is the back left and the trans sits on the right side of the engine/car). Shouldn't the shop have noticed if this were the case?

The core of my question is really, are there any steps I can take to properly diagnose this?

I don't want to do a trans rebuild since this is my daily for now. I don't trust the shop for other reasons, so even if they warranty their work I'd rather do it myself at this point. I still have my old transmission and if a rebuild kit is cheap, I might attempt doing it on that one since it is already out of the vehicle.

Any help is appreciated.

 
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Step one: check the level.

 
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Step two: Check the ball at the bottom of the shift lever. Sometimes they split and get stuck causing it to pop out of gear.

 
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Update: I had to drive the car today. On the way home I started to get the same behavior from 4th. This seems to indicate it is not internal, in my opinion. Hopefully its just something to do with the linkage.

Yeah. I will start there once I get my other ride ready. Probably tomorrow.

I will look into doing this. I wonder if this is more likely, since I lost 4th today.

 
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Maybe. It happened to me 10+ years ago. I either had problems staying in third or fifth, I cannot remember. Sprayed with silicone lubricant and never had to touch it again.

 
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So the ball is split down the middle. It definitely looks like the forward gears travel further from center to engage. The back ones, 2 4 R, split the ball when I pull on it. However, they look like they are going in gear with the engine off.

 
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Try lubing it, otherwise you need to replace the shifter

 
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So I pulled the center console apart to look at the shifter assembly. I went into all the gears with the car off. I do see the ball split a bit when I pull into the back gears, but they seemed to go fully in. I sprayed some lithium grease and wiggled the shifter around and went into the gears several times. After that I drove it and I had no issues with it staying in gear. I wonder if the dust boot was restricting movement somewhat. I didn't put that back on yet.

 
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have a new ball ready to go in when it worsens
I would think a ball splitting would hurt a lot [joke!]

 
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So this issue has returned. However, it has not been a year+ of driving since I had her sitting for a while so I could replace the head gasket. I don't think that the split ball at the base of the shifter is the culprit. All of the used ones I have seen have the same split, it seems to be manufactured that way.

So far it has only returned in 2nd gear. It will go into gear but releasing the clutch pops it out.

I went down a few avenues trying to figure this out and they are as follows.
1. The shift cables are loose or worn.
-I couldn't determine if they are worn or not but the cables are attached and secure where they aught be.
2. Transmission mounts (passenger and rear) are worn and allow the transmission to shake too much preventing it from getting fully into gear.
-I replaced the driver side and front mounts recently for other reasons so I didn't revisit those.
-While replacing the passenger side mount I noticed that the bolt holding the mount to the transmission was not threaded in and only held by JB weld. The shop I had put in this transmission is shady and I have found many mistakes by them since working on the car after them. I hope that the two nuts will be sufficient because I don't have a solution for this.
-When replacing the rear mount I noticed that the bracket that connects the mount to the transmission was missing a bolt, it typically has 3. Additionally, both of the bolts are m12x1.25x70 when the parts catalogue shows that these should be m12x1.25x60. Why one was missing is beyond me, I chalk it up to shady shop. I purchased new bolts and installed the new mount either way.

After doing the mount I took it for a drive and I had no issues for about 25 minutes. As I was headed back home she started to pop out of 2nd every time now. This leads me to avenue number 3.

3. The aforementioned shady shop may not have used honda fluid in the transmission. Since the issue only started to reappear after some drive time, I think it has to do with fluid viscosity at temperature. I know some transmissions can be finicky with the fluid you put in them. I have 2 quarts of honda fluid to replace what is in there and I will try that tomorrow. Maybe 2nd gear is the only one that is causing a stink since it is the most worn in general. I am not sure why just 2nd but after this I am out of ideas.

 
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Changed the fluid today and the honda fluid still had it popping out of second within the first few minutes. It would only stay in if I shifted at a low speed and gave it a bit of rpm. Any higher speed shifts into second, such as starting from a red light, wouldn't work.

I am at my limit. I am not sure where to go next.

I could replace the shift cables, but at what cost. A few hundred or gamble with a scrap yard set.

I could replace the shifter itself, but I don't know how to even test if that is the issue.

I still have the old transmission which I could rebuild on the bench, but I have never done that before. Maybe I could take the trans to a shop to be rebuilt, but again is it worth the cost.

 
Rep Power: 367

try going to a shop for opinions? You don't need to have them do the job, just diagnosis

 
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I thought I would give an update here since it has been a while. Through the holidays I didn't do anything due to cold and travel to see family.

I got back into her in January with more motivation. Here is what I did. I relayed this problem over on d-series.org, which seems to have some more enthusiast minded folks so I figured I might dip my problem in over there. I got a few replies:
1. Shift linkage bushings.
2. Shifter assembly bushings.
3. Try different fluid
4. Replace the gear selector detent springs
5. Crack her open and do a rebuild.

I listed the steps in order of difficulty. I went and looked at the linkage bushings where they connect to the trans, and they were rather tight. The ones on the shifter side were destroyed so I replaced them, like $8 on amazon. No joy on the fix though, but still needed to be done. The bushings where the shifter is bolted into the car were solid so I left those alone.
After some reading I found many people swear by the GM AC Delco synchromesh fluid. In addition there were a few instances of stiffer detent springs solving the issue. I decided I would do both next. I chose this order because I looked at the old trans in my garage and the snout where the throw-out bearing sits was completely gone. So that a non-starter for me.
After doing the fluid and the springs I went for a test drive. 10 or so minutes into the drive I turn a corner and my clutch goes to the floor. Pull over and check the hood to find brake fluid everywhere. Sure enough there is a line burst in the clutch hydraulics.
The following weekend (this past weekend) I replace the three clutch lines (master to hose, rubber hose, then hose to slave). These lines are odd *****.
Master to rubber hose is a 1/4" line with an M12x1.0 fitting. Then from the hose to the slave the line is 3/16" with a 3/8" fitting. The 3/16" line went in well enough but the fitting that came on it wouldn't seat right in the slave cylinder. I removed it and reused my old fitting.
I couldn't find a shop that sold 1/4" line with a metric fitting, or even an adapter or a fitting that I could put on. Closest was an M12x1.5 fitting. So I went with a 6mm line and an M12x1.0 fitting instead. 1/4" is 6.35mm so the size difference might not matter. I flared and bent my lines which was a PITA because of the way it is.
I also learned that the bleeder valves are utter crap on these, at least when trying to use a vacuum to pull through them. It was way faster to put a nozzle on the vacuum pump and stick it into the bleeder hole with the valve out so I could put a couple reservoirs through quickly, then put back the bleeder and have a helper finish the bleed by foot.

All this said and done I went for another test drive today. The entire drive I was in and out of 2nd gear, through up and down shifting. This was in a neighborhood so I never got up past 40 mph, but I figure since second is my problem child this is a sufficient test. There are hills where we live so I ran the gambit. It was a full 25 minute drive this time so I think that should be enough time for a full heat soak of the fluid. At this point I am happy with how she drives. The springs and fluid may not have been a permanent fix, and I might be back eating my words when I find out a rebuild was necessary. Hopefully that is later than sooner. However, for now I want to just drive her and enjoy the car.

Happy to answer questions about what I did if I glazed over them in the process of writing this.

 
Rep Power: 367

glad you found a potential cause! Thanks for coming back to report your finding!