There is no seal or "O" ring on the counter shaft, just a freeze plug looking plug at the front of the case that sits in a 1/16" recess. Usually on reassembly some high temp RTV gasket material is applied. Are you sure it is the countershaft and not the front bearing leaking? Have you had it apart recently?
Vince, I do not think there is any kind of a plug there. I think it is just the countershaft. And yes I am very sure it is the countershaft leaking and not the bearing. It has about 16000 miles on rebuild. It had only been back out because of defective clutch.
Clean the shaft end/case area with Brakleen and use some super Hi-temp silisone sealer on it. GM used to (back in the sixties) sell a paper gasket that covered the front of the trans to belhousing area. I haven't seen one in years.
On the stock muncies there is on plug at the end of the counter shaft. Only the aftermarket cases have the freeze plug feature. I have been rebuilding these transmissions for 20 years and this leak is the single most common problem i have found. Like BOBCRMAN stated you can usually get a good result by sealing the end with some RTV. I usually clean the area real good with brakecleen, make sure there is no oil on it at all. Then i fill the small recess with silicone. But if the case is worn and the counter shaft is a sloppy fit it will leak no matter what you try.... I bore the cases out and install a steel steped bushing in it. This eliminates the leak 100 % of the time.....
k-star is right, my oops. The OEM Muncie cases had a beveled hole in the front of the case that wedged the countershaft foward as you bolted the rear plate and extension housing on. Unless the countershaft has spun and elongated the hole, some rtv should solve the leak.