Grinding noise coming from manual transmission in 3-5 gears?

Has the transmission fluid ever been changed? This SUV should have the transmission fluid changed every 48,000 miles according to Schedule B of the Owner’s Manual, and requires ATF+4 fluid.

I agree with all of those ideas except 5), and the simplest and cheapest to check is the fluid/lube level. Low fluid will cause gear noise, which is accelerating transmission wear.