(Assuming you have an HD Hero)
For #1: What PC are you playing it back on? I have an old Macbook, and it will not play the 1080 vids due to it's slowness....it takes a bit to play these back. Suggest re-encoding the video to something like Divx...that should smooth things out. Or...just record at 720. Keep in mind that when recording directly, the speed/cpu use on the video is not as optimized is it could be by doing a post-recording re-encoding. I use a tool called TMPGEnc, but I'm old-school so there are likely better ones out there.
For #2 - This is normal. The SD Card is Fat32, so it cannot deal with a file larger than 3.8gb. Just stitch them together in post production. This is discussed in the manual/leaflet thingy. Get your your microscope to read it.
#3 - There's a good thread on this here:
GoPro Video Camera. Read through this thread...there's some good comments in there on the audio issues. I use that same recording device for my audio.
Hope that helps...
Dan