I know my transmission has a bad bearing. I would rather see if I should replace the transmission if it is an internal bearing or just do the clutch with the bearing kit. In gears 1, 2, 3 the sound is most noticeable and increases as speed increases.

The sound occurs when:
- In gears
- In neutral, with the clutch pedal out (more of a howling bearing at a constant pitch)
- When the car is on a lift, with load on the car (braking) (wouldn't make the sound without the load of the brakes)

The sound goes away when the clutch pedal is pressed in

I also have a known good transmission from a D17A2 VTEC (Si) ... Will that work besides the different gearing?

 

yes most likely a bad input shaft bearing (this is the first to starve for oil when low ,and they go bad even when oil level/condition is ok) ,when you push in clutch the input shaft stops spinning and noise stops.

here's a great DIY replacement with video's
DIY: Input Shaft Bearing - Honda Civic Forum

 

this is corerct. it's an easy fix if you have the time and enough mechanical experience.