Yes, tranny fluid is in the tranny, but air in the clutch lines could be causing the problem.

Don't flush the cruddy fluid thru the system. First, suck the old fluid out of the reservoir with something like a turkey baster. Then don't ever use it in the kitchen again...

Tie a string around the clutch pedal so your helper can pull it back up from the floor. Fill the reservoir, put a rubber tube on the bleed valve (on the slave). Open the valve by turning it about 1/8 turn while he puts the pedal down. You close the valve, then he pulls up the pedal. Do several strokes & check the reservoir. DON'T let it go empty! Keep doing this until there aren't any more bubbles. You'll have to pump maybe a pint thru it?