I've also had low audio reports on my FT-3D. I have noticed that my pinky falls over the mic hole. That said, even when I use the radio left handed and mic gain at 9, deviation set to wide, I still get reports of low audio on analog only. I've noticed the same when receiving other stations who have this radio. I did some testing on the radio, listening with another HT on simplex. If I speak right into the mic hole, the audio is loud and clear. If I hold the radio the way I naturally would, audio is low. If I cover the mic hole with my pinky, audio is non-existent. My observations are that the mic hole is really low on the radio and I tend not to speak into it. Most people hold the radio so that they are speaking into the display or badge where is says "Yaesu". If you do that, the audio will be very low. You must get in the habit of speaking into the mic hole and also not covering it with your pinky. I wish Yaesu had put the mic higher up as holding it so as to speak into the mic properly is a bit unnatural. Again though, if you get in the habit of speaking directly into the mic hole, it has plenty of audio.
I've also noticed that the receive audio sounds much better on digital than analog. Analog is very tinny sounding out of the speaker. This is not the case with other radios I have. It seems Yaesu really tuned this radio for digital modes. I do like the radio overall, it just takes some getting used to.