There's the neutral indicator shaft and shift shaft that also come through the left side of the case. Check those also.
I'm pretty sure they can all be removed and replaced wit the engine still in the frame. Clean everything well and take a Scotch Brite pad to the countershaft BEFORE pulling the old seal. You'll want the shaft as clean as possible while putting the new seal on and put some tape around the splines so they don't cut the new seal as you slide it on.
To remove the old countershaft seal, put a couple sheet metal screws 180 degrees apart into it, just a few thread in. Then use a couple pairs of pliers to just pull it straight out. Probably not relative to your ordeal, but the Suzuki DR650 motorcycles had a tendency to physically blow that seal out of the case, so the new ones have a small keeper over it to prevent that. Maybe it got too much oil at some point and the seal became unseated?
The story of three wheels and a man...