The clutch line is wet and hooks up to the slave cylinder on the bell housing. It is completely separate from the fluid in the trans. You need to bleed the clutch (the master clutch cylinder is hooked up to the brake reservoir right?) by hooking hose from the front right brake bleed nipple to the clutch bleed nipple. Crack both bleed nuts open and slowly press on the brakes about 3 times. Tighten the bleed nipples and see if you get resistance.
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