Diesel Bombers - Transmission issues wont stop

So im on way to work this morning at 430 and i realize i forgot something at the house, so i turned around at the gas station and pulled out in second, wasnt hard on it at all, i shifted into 3rd and next thing i know im hearing something banging around down there, i dont think i lost the gear, so i pulled off called a ride and came home for a bit till the local shop opened, went down with them to look at it started it up in neutral and every so often i heard something hit down there the sound was faint, so i pressed the clutch in and tried putting it in third and when i tried putting it in i could hear it and feel it in the shifter that something was hitting, so i got it towed to the shop and thats where it is until they look at it, i just recently had the mainshaft replaced about 2 months ago and havent been real hard on it sense then, but now im wondering what you all think is wrong, i did drive it a tiny bit, skipping 3rd and going from second to fourth and i could feel the clunking a little bit at the bottom of fourth

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