I don't see how it would be leaking up there. There is no pump in that 5-speed. The gears are simply immersed in oil to the level determined by the fill plug. You might try draining the fluid, making sure the car is level, and then filling until it runs out the fill opening. I hate pumping fluid in so I pour it in from the top thru the shifter linkage opening. Let it sit until the fluid level settles down, then bolt everything back up.
As far as leaking around the shifter, how is fluid getting up in there to fill that area up so that it will leak? If the tranny is overfilled it will certainly leak as when it gets warm, fluid will be forced out. But filled properly, leaking is not common, and is actually quite difficult to make happen. The rear seal usually will only leak if you park pointing up a pretty steep driveway or hill. There's no fluid being pumped around inside that has to be contained by a seal...
BTW, the reason for the silicone around the shifter is not to keep fluid in, it is to keep water _out_...