Forty feet of flex conduit isn't legal (NOTE/CORRECTION: The length limit statement is incorrect and was brought to my attention by Mikey. There is no limit on FMC.) but you could use prewired MC (the new version of BX).
I have run 1" PVC through joists on 16" centers but it is diffucult. You can run 1/2" PVC conduit through studs almost as easily as flex, and it is easier to get the wire through it. Put the PVC out in the sun for a while to make it even easier. Just be sure you run a line to make the holes in the studs line up.