I can tell you that your lens is glass simply because it has the sorta holographic film under the log that all the newest glass lenses have. They used to just have a metallic silver film. Also, if you have a normal GBA with a plastic lens, you can compare by tapping on the lens with your fingernail of each. A glass lens produces a distinctly different tone
Getting these things 100% lint/dust/debris-free is no easy task. Even if you manage to clear out teh fleck you see right now, it's entirely possible for another to get in. The GBA is not an airtight machine. The problem is that the mod requires removal of the 2-sided foam tape which surrounds the original LCD. It's purpose, beyond keeping the LCD in place, it to prevent dust from getting in between the lens and the LCD. I've never seen another modder replace the tape after modding the shell, but we have started doing so and it helps a TON! If you're up for taking it apart, I would very much so suggest throwing some thin, 2-sided foam tape around the perimeter of the LCD before re-installing it.
If you just want to try and get rid of the dust that's under the lens right now, then yank the lens off with a suction cup (you'll prolly need one at least 1.5" in diameter to provide enough suction), remove the dust with either canned air or a DRY Q-tip, then make sure no dust has settled on the lens, and replace. If you use ANY cleaning agent, whether it be water, Windex, isopropyl, or whatever, you'll find out that it's even harder to remove the film/smudges left by it than the dust itself.
To sum it up, if you can deal with the fleck of dust, then I would highly suggest leaving it be
Thanks for the tips!
While you are here, perhaps you have some insight on this one...I'm noticing while playing certain Gameboy/Gameboy Color games, at times the LCD will flicker, almost in sync with the music. Any idea what the cause of this is? Seems like a power draw?