After replacing the battery (IF108-063-2) I found the trackpad click pressure to be noticeably higher. The plastic frame on the replacement bowed out some just above the logos below the center cells, pressing on the trackpad once the lower case was reattached. I used some gentle heat from a hot air gun (I used about 150º C) to soften the plastic and bend it back down. This reduced the pressure on the trackpad.
To elaborate on Daniel’s comment, particularly the middle 6mm screw seems to have a lot of range and can be over-tightened. I stopped and backed it off a little when it appeared to be deforming the cell to the left.
I found that using a scraper blade was the easiest way to get under the glass, both for broken and unbroken areas.
I just got finished with replacing the power/mute/volume assembly in a wifi ipad 3, and I did not find that removing the headphone jack assembly was necessary. Just unscrew the rear camera so you can pivot it out of the way of the power switch, but it can stay connected via its ribbon cable.
Also, when reassembling I found that I needed to be careful about over-tightening the screws around all three buttons. If they were too tight they wouldn't click properly.