Helix - right off the bat, a few thoughts come to mind. Check the individual frames of the stack if the images are in focus the problem lies with your stacking program. If the individual frames are out of focus then you have an equipment issue. Right off the bat:
1) Are you using live view to shoot the stack?
2) Are you giving the WeFine macrorail sufficient time to settle between shots?
3) What material is the tripod made of, aluminum is more susceptible to environmental vibrations then carbon fiber or wood.