helped a guy install a new ta. put tractor back together and when running we get gear noise in 1st and 2nd not 3rd or 4th just sitting in neutral.louder clicking in 2nd. tore back down and allgears on bottom shaft are right. top gears and forks are right. you can turn input shaft by hand and get clicking in 1&2 but goes away in 3&4. ANY THOUGHTS ON WHAT TO LOOK AT? THANKS.
 

Does it click once for every revolution of input shaft or one revolution of lower shaft or click constantly? Those are things you have to determine. Might be gear spacing on lower shaft is wrong due to spacer on lower shaft in wrong position.

Another thing is when the gears on lower shaft wear on spline they form a pattern. If you tighten lower shaft nut it cocks those gears. I always tighten nut, loosen just enough so gears are free to wiggle a tiny bit. Then locktite the nut so it cannot come loose. Others won't agree but that's ok, it works.

And then, realize that over the years, ratio's were changed and then tooth angle was changed from 20 degree teeth to 25 degree angle teeth. All have to match. A few things to look at, not all of course.
 
Did any of the gears get replaced or put in turned around all those things can make it change the sound. Gears wear as they run and one turned around could cause such a thing. Would it hurt it probably not. Bother you because of the noise yes. Back 40 plus years ago we had our MD transmission apart and put the reverse idler gear in backwards. It looked the same on both ends with the same number of teeth and everything. With it put in backwards there was no second gear. Everything else worked fine just no reverse. I think it also had a noise. Flipped around and noise went away and second gear came back.
 
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