Manual Transmission Noise

eManX
2012 Mazda 5 Sport 6 Speed Manual 70,000 miles
Rotating noise coming from the front, louder in gear than in neutral, sounds the same no matter which gear, gets louder with acceleration, noise is consistent at cruising speed, gradually gets louder so I hear it sooner at lower speeds after each drive, can hear it coasting in neutral coming to a stop whether clutch is engaged or not.
I took it in a few weeks ago to the dealership, and the technician could hear the noises. He jacks it up and recreate conditions and there is no noise at all. It just suddenly stops. I drive it a few weeks and the noise slowly comes back same as before.
I take it back to the dealership, they jack it up and recreate conditions. They say noise is loudest inside transmission. They drain the fluids and find no metal shavings. They refill it with proper transmission fluid. They tell me it is absolutely coming from inside the transmission, but have no clue what it could be. They were expecting to see metal shavings in the old transmission fluid, but completely clean. They then quote me for a new transmission.
What could it be? Is it just a noise? Is it dangerous to drive? Is it really the transmission and not the clutch or something else? I'm in Tampa, FL; and we've been having crazy weather the last few months that coincides with this dilemma. Literally drives perfect every time, smooth shifting, no stalling, everything is as if it just came off the lot except for this new noise while in motion.
If it is the transmission, what would you suggest? Dealership says $3,500 for new tranny and $500 to install; however the guys there suggested I grab a used one ($500 to $800) and will install it for the same price. The dealerships will not rebuild a tranny. Should I get a new or used tranny and have it installed or find someone to rebuild it? Should I just risk it and drive until failure?