What engine are you working with? You usually see counterbalance shafts in big 4 cylinders, where they are put there to smooth out vibrations (to sell more cars).
Although I've never done one, I've read about this old hot-rodder's trick with engines that use a separate chain to drive that countershaft; Just cut off and remove the chain, and abandon the shaft in place <leave it in>. You do have to be careful, to make sure the counterbalance shaft and drive chain don't also drive some crutial accessory, like the oil pump or distributor
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