You will not be able to fix the bearing noise with new lube. I have seen cases where the noise got worse after the lube was changed. That being said, the Amsoil MTG is a very good lube. I think your idea of a drain and refill with MTF is a waste of time and money. It won't hurt anything. I would just fix the bad bearing and then put in the MTG.
A bad input shaft bearing that is making noise should go away when you put it into whatever gear is 1:1 ratio (power flows straight through in 1:1) In a truck I had, that gear was 4th gear, not 5th, which was an overdrive. When in the 4th gear, the power flow was straight through the input to the output shaft, and not down through the countershaft. When in 1st, 2nd, 3rd, and 5th gears, the power flows from input to countershaft and back to main or output shaft, which puts more load on all the bearings supporting these shafts, and makes noise if those bearings are bad.
If the throwout brg is bad, it will be noisy when you push the clutch in.
You will not get any better lube into your bearings by going thin. If you want to experiment with lubes to quiet your noise, put in a load of Lucas trans fix instead of going thinner.