I know this is old, but I have been having the same problems. I have a repair business run out of home, going on two years now.
I have been using permatex brand silicone RTV, the regular "sensor safe" blue kind. Not the "super blue". It comes in a regular blue squeeze tube, not silver (that's the super blue).
You MUST use the sensor safe kind because regular RTV silicone has vinegar in it, and the fumes will corrode metal, and thus corrode electronic circuits, ruining the device.
I have had good results applying just a little bit around the perimeter of the frame. Once the glass is laid down, I clamp it with clothespins all the way around, about 30 clothespins. If you're very careful you should have little or no RTV squeeze out of the edges (and hope to god you don't smear it on the inside of the glass or LCD). I use dentist picks to run between the glass and plastic trim to remove excess RTV, but there will always be a little blue color left by the RTV. This annoys me, and I wish there was a clear silicone RTV that was sensor safe, but no customers have mentioned it. Let it sit 24 hours (another bad thing sicne I am known for fast service, and people don't like not having their device for this long).
Clamping, RTV's lack of sponginess compared to 3M tape, slight variations in the height of the areas the glass sticks too, and thinner glass than OEM will cause the glass to have some waviness to it (it will flex the glass a little bit) but it's not noticeable except at an angle. I have had a problem once with the glass touching the LCD, it was bowed inward slightly. I tugged outwards on it with a suction cup and the visual distortion caused by this touching went away luckily. I'm afraid I may have customers notice this reoccurring over time though. Seems like the replacement glasses are usually thinner, and not tempered as good as OEM. But what can you do?
-Brent Dennard