1999 Mazda B3000 transmission whistle

So I recently replaced my clutch in my truck, most of it went pretty smooth. Except that I didn't replace the pilot bearing. After I started it up it made this whistling noise in the transmission. I know it's not the engine because it can be heard directly at the hole in the bell housing of the tranny. I drove it around and every once in a while it's there, but goes away eventually. If I go on long trips it goes away completely, until I drive in the city for a couple days, then it's back. If I let the clutch out enough to wear it almost dies, the noise goes away until it's fully engaged and I'm moving. It makes this noise whether I'm moving or at idle. The rear main is also leaking a little bit (not sure if it would affect anything) but it's a little irritating because it didn't do this before. Just wondered if it's the pilot bearing or maybe something else? Any help would be greatly appreciated. Thanks!