Bought a 2001 ls1 and 6 speed for a 69 chevelle project I am working on. Converting from auto to manual found most hardware from great site "musclecarsonly.com" but am having problems with hydraulic ls1 clutch to 69 chevelle mechanical hardware, anyone did this before?

You should be able to find that information on this site. http://www.ls1tech.com/forums/forumdisplay.php?f=28

The truck pan looks like it is about right to clear the Chevelle cross member.

just use a Weir Hot Rods product kit, then get a smaller MC and attach it to the cluth pedal.