So I’ve put in a few oil seals in various bikes over the years and not had any problems. I’m having a heckuva time getting one to work on the shift shaft of my DT3. When I got the bike last fall, it leaked a little, nothing major. As I’ve been working on it this spring, I replaced the countershaft and the shift shaft seals. They were part of a set on a red card that was on that giant auction site. I pretty much knew right away that I would be redoing the shift shaft, as I didn’t remove the footpeg bar and it was in there cocked to one side. So I got a new oem seal, took the footpeg bar off, removed the old seal, and used a deep socket to drive the new seal in place. (16mm socket, if I remember right). Still leaking oil from the shift shaft…. I guess my question is, can you drive the seal into place too much or too hard? I’m thinking this is the problem now but wondering if this makes sense?
Thanks for any and all advice!

First thing I check is make sure the transmission vent hose is not blocked. Not sure why, but 7 out of 10 times that I've had a shift shaft leak, the vent is plugged. One bike would actually push out the shifter seal after riding.

And sometimes oil can be dripping from shifter and it's coming from someplace else... can be hard to ID the source sometimes. I clean the whole area... then if the leak happens just sitting, I let the bike sit until it leaks and then dust the whole area with baby powder or fine flour. Sometimes this reveals a faint trail of oil from up higher. (Same thing can be done if leaks after a ride... clean, ride, dust, inspect.)

Or these days you can buy a kit that has UV dye that you add to oil... then you can find source of leak with black light.

Two  of the most overlooked procedures in seal replacement are:

The bike leaning too much to the
left from a kickstand mount that has excessive play. The kickstand should fit tight on the mount with less than 25 thousandths of free play. Secondly, a block of wood under the kickstand helps prevent the bike from over leaning left. Standing on the bike with the kickstand down kick starting creates this excess free play.

Most important factor in installing oil seals is pre cleaning. I take several minutes with a few Q Tips and circle the perimeter with wet rubbing alcohol. Dry seal installation with nothing on the seal. Clean the shafts the same way - well too. Clean the oil from your finger tips on the outside of the seal and use your opposable thumbs to press fit in in firmly. 

Vintage Bikes Leak Fluids. 

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Thanks to you both for the thorough responses. Mark, if looking at the Crankcase diagram, that would be #12, crankcase breather, right?
Asco, thanks for your input. For some reason, I thought i had heard it was good to put a light coating of fresh oil on inside and outside surfaces… I probably have the current one in there so hard, the I.D. Is curling. Can’t see it to tell, but wouldn’t surprise me…

Yes, hose sometimes gets clogged.

(I always lube seals when installing...  inside for sure...  on something like a crank seal where pressure pushing out the seal can be an issue I might use a thin coat of blue loctite on the OD.  Or soapy water...  some recommend Windex... But I often just use a little oil or silicone grease on the OD.  To each his own. )

Thanks again, Mark! I will try the breather hose first

Here's a decent article on seal installation.  baartgroup.com/oil-seal-installation-how-to/

And a quote from the article:  "When installing rubber-coated seals, apply lubricant to the outside diameter as well. This will help prevent the seal from rebounding or backing out from its mounting place."

Most Yamaha seals are rubber coated on the OD....  sometimes you do get a metal OD seal that may or may not have a factory coating on the OD.  No lube needed on the outside of those. 
 

Thanks Mark!

Phyllo, had you considered it might not be the seal that is at fault causing the leak.  Suppose the shift shaft itself is bent such that over its 15-20 degrees of rotation it might put uneven pressure on the inner lip seal. Just a thought.  Anyway hope you sort the leak soon, Andy.

I think all of these tips and ideas have merit because seals either work or they leak for many reasons
I have had issues with my bikes that have clutch release coming in the bottom - DT360A and DT400E - dripping a drop or two.
On these I cleaned bore with brake cleaner and Qtips, then put this stuff on ID of bore and grease on ID of seal and leak fixed.  I think the very minor scores or distortion or whatever were filled by this stuff which acts as a lube before it sets up and seals I think???!!!!  

www.amazon.com/Permatex-80062-High-Gaske...%2Caps%2C141&sr=8-15