It sounds to me like you missed the "shifter knob" on the shift shaft when you installed the transmission back into the case. If your transmission was shifting correctly on work bench, it should at least shift from first to second gear.
You're going to have to pull the transmission back out of the engine case. With the transmission out of the case, look into the the transmission cavity and hold the shift lever so that the short shift arm is level parallel to the bottom of the engine case. Mark the outer end of the shaft so that you can verify that it is still level once you get the transmission back in the case.
Now, put the shift lever (lever you shift the transmission with) temporarily on the shift shaft and support it some way so as to hold it level. Install the transmission. Now, before finishing the installation job, check to see if the shaft is still "level". Install the four bolts that hold the "acess plate" of the transmission in and try to shift through all the gears by turning the mainshaft and having someone hold or turn the countershaft. Make sure the transmission works before you finish up the job.
If the transmission still doesn't shift. Take it back out and work with it in a vise until you figure out the problem. It'll probably be something to do with the shifting mechanism rather than the gears.
Good Luck
Steve
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