Noise from gearbox only in 5th gear

Hi all, my lockdown project has been an engine rebuild on an 81 XJ650. All back together and everything is great. Except...when (running on the center stand) in 5th gear, clutch lever let out, there is an intermittent, loud, metallic clunking (or clanking?) noise. The noise seems to be emanating more from the left side of the bike.
Is it possible that this is due to a bent shifter fork coming into contact with the rotating cogs? First, second, third and fourth gears are all solid with no odd noises. Neutral seems fine and normal too.
I had the forks out and inspected them and one of them was showing wear and a bit of burring, which I gently filed off, then refitted.
The pics are of the box when I first split the cases and you can see the discolouration on the middle fork.
Any suggestions? It seems such a specific set of symptoms...
Cheers to all

 

U-joint. Check it.

 

Cross-Joint:

sdp2) Original or rebuilt "U-Joint" or CROSS-JOINT perfectly replace worn or damaged original piece. The U-joint takes quite a beating during its life----and should be replaced if damage, wear, or excessive play is noticed. The last thing you want to have happen to you, when you're tooling down the freeway, is to have this cross joint fail!

Driveshaft Cross-joint Evaluation:

Is this you?:

"Everybody should go check their u-joints before you have my problem. I admit I like going fast, and doing hard starts. And it caught up with me.............my u-joint was within a few miles of complete self-destruction before I caught it, and the removed u-joint is scary. So if you've got over 50,000 miles on your bike, then this is critical!"

Here's how to check your driveshaft u-joint:

a) Put the bike on the centerstand, and put in 5th gear. Rotate the back tire back-and-forth. There should be minimal slack. If there is more than 1/2" of rotation, you may have a serious problem

b) Pull the swingarm boot on the shaft back as far as possible, and use a flashlight or a finger to probe for metal peelings on the arms of the joint. If you can feel shards or what feels like bent metal, replace the u-joint ASAP!

c) If you feel a vibration that shakes the whole bike, pull over and get the bike towed home. It's worth doing that, rather than ending up with a destroyed crankshaft, u-joint, driveshaft, or worse!

 

Thanks, I’ll do that next!

 

As someone with ZERO experience with shaft drive, but lots of experience with mechanical things, I have a question: OP says it only happens in 5th gear.

If it was a driveshaft/final drive issue, wouldn't it happen in other gears as well, at least in 4th?

 

The shifter forks run in the grooves they would have to be catastrophically bent to hit the teeth of the cogs and then surely there would be gear selector problems. I was thinking of shims in the driveshaft crankcase joint but if there were excessive play due to that it should affect all gears. Did you replace the rubber seal between the middle drive shaft and final drive which keeps oil in the bevel gears under the gear selector cover.

 

It depends on how bad the u-joint is.

 

If the U joint was on the way out would it tend to oscillate the degree depending on how much it was worn?

 

Essentially. At least in my experience with u-joints in various applications. Keep in mind that suspension compression (or lack thereof) plays a role, especially given the very limited range that the XJ u-joint has.

 

Thanks for the input everyone...I’ve checked the ujoint best I can and really can’t see it as the problem.
After really close inspection of the XS1100 transmission video that’s linked one of the threads, I’m thinking my problem might be that the pin on the base of the middle selector fork is worn.
Does anyone know if you can change the selector forks by accessing them through the sump opening?
I’m pretty sure the output shaft can be removed that way...
TIA

 

When I run my bike though the gears on the center stand it vibrates. But is fine when driven on the road. Do you get a vibration when riding?