1/ see the attached vi : you can separate the Y component of the waveform, for each channel, and average it.
2 & 3/ If you need to open your file with a spreadsheet application, such as Excel, I believe it is much better to stay with data organized as rows, instead of columns, specially if you have to work with 1000 elements !
Anyway, since in 1/, the Y column was separated, you can simply save the averaged values as in the attched vi.
CC
Chilly Charly (aka CC)