The countershaft in your trans looks used. Do yourself a favor and replace it with a new one. Get the Countershaft Arbor Tool from Brewers and a brass drift. If you are good, you can take the bolts out of the tailshaft housing and rotate it and drive the old countershaft out while sliding the arbor tool in at the same time. Then do your clean up of the countershaft bore and slide the new countershaft back in, pushing the arbor tool back out the front. As soon as the countershaft starts into the front bore, do as Dan says and clean the bore and apply the silicone. Then drive the countershaft the rest of the way in. It is a press fit. When the silicone has hardened use a single edge razor blade and remove excess silicone flush with the front face of the main housing.
http://www.brewersperformance.com/proddetail.php?prod=CS-T