Question? When in the small ring front and in 3rd and 2nd from the big in the back i get a clunking noise. I went through and adjusted my low and high limit on the rear deraileur but it hasn’t helped this problem. It only does it in the small ring. Im a little puzzled on this one. Chain is free and all links look straight. I don’t see any problems with the rear cog. It only does it ever other pedal stroke so i thought it might be the chain but i don’t see any problems with it. If i shift to the big in the back then back down into the 2nd or 3rd it doesn’t make the noise, sometimes. Don’t spend much time in the small ring but when i did i started to hear this. I also can recreate it on the bike stand.
Not uncommon, should just take a turn of the barrel adjuster to fix. The barrel adjuster is or should be right next to the derailleur and the cable runs through it into the derailleur. Spin up the crank (keep spinning it) until you hear the clicking and slowly turn barrel one way or the other. If it starts clicking faster when you are spinning it turn the other way until it goes away. Then run through your gears to check shifting is good. Takes about 30 secs normally.
Ok thought if I did all my adjustments on the big ring I would be good on the small. Lesson learned.
Is the cassette loose? I had something similar last month when the cassette got loose during somehow. Quick tighten up and all was good.
I just total started from the start with tuning the rear so far everything sounds ok. I think I’m in the need for some new cables also.
I’ve had a similar issue. Over the past few months I’ve had an increasing issue with noises from the back wheel area.
I do all my own wrenching. I have been busy recently so just put up with it. This past weekend I set aside an afternoon and headed to my bike shed.
I took out the rear wheel, cleaned, relubed and adjusted the wheel bearings. I removed the cassette and freehub, cleaned and lubed everything an put it all back together and re tightened the cassette. Then for shits and giggles I tore apart my pedals (cheap Exustar SPD’s) and cleaned, relubed and re-tightened them too. I took off the deraillieur jockey wheels out and gave them some love too. Chain got a good clean and lube just because I had some time left.
Guess what? It fixed the problem. I don’t know which of the bearings was the problem but the noises have all gone and now I can ride for several months without having to devote another weekend to bike maintenance. Try that to see if the nose stops. Adjusting the limit screws at the front won’t make any difference. Adjusting the limit screws at the back won’t make any difference either (they only affect 1 and 10/11 depending on your gears but not 2 &3) Barrel adjuster at the deraillieur will be your issue. Or a bearing or a pledal or a cassette 
1 bike down, 11 more to go. Damn. (Sooner or later I have to learn how to rebuild a Sturmey Archer 3 speed hub, so I can restore my Raleigh 20. Does anyone know any good leads on information on Sturmey Archer rebuilding?)
I know this may have nothing to do with your problem, but years ago I too has a click every turn of the cranks when in the small chain ring in particular gears.
Every thing was cleaned, everything was adjusted…
took it to the LBS, put it on the work stand & spun it in to the offending gear…
their solution was to push the front derailleur cable, which bad bent the wrong way, away so it was no longer hitting the right side crank every revolution.
Whilst in the BCR, the cable was pulled tight so it was in a different position… so no clicking.
embarrassed or what?
hope your solution, embarrassing or not is as simple.
Ha! I can top that. I was pretty pleased with myself for replacing my own chain. Until it came to light that I had put a 9-speed chain on a 10-speed drivetrain. Ughhh…
Giving the barrel adjuster is probably a likely fix (could I qualify that a little more??) but if that doesn’t do it then replace the cable and the housing at the der. (at a minimum, maybe it’s time to replace all the housing). Often that last section of housing collects grit from the road/rain and gums up a bit. This causes the cable to hang up a little when shifting back and forth, that’s why shifting up and back down fixes the issue. Also, the advice to overhaul the drivetrain is sound this time of year, it gives you a chance to start the real road season with everything lubed and working properly and you can do all the inspections on parts and frame that we’re supposed to do:)
rich
I also had odd clicking noises coming from my hardtail MTB and when it was new which wasn’t the drivetrain parts itself. Trying to hunt it down I noticed a bunch of small stickers on or near the disc brakes which I did remove…some of the noises went away. Still had another one that clicked every full rotation of the crank arm…turned out there was another sticker in that area that had a “ducktail” of sorts sticking out and flapping everytime the crank arm passed by. Removed that and finally all the clicking went away…it was probably after maybe a dozen rides on that bike I finally discovered all the stupid factory stickers that made noises like a playing card in the spokes thing I used to do with my Huffy as a kid. It’s hard to pinpoint where the noises came from riding unpaved trails trying not to crash into a tree or something. Finally was able to narrow it down when I did a couple of ride with that bike on a paved trail.