Be sure to look under the dash on the firewall for a leak too. On FJ40's, there is a clutch adjustment procedure which involves pedal height, pedal freeplay, and freeplay at the adjustment rod at the slave. Pedal height and pedal freeplay involves the stroke of thr master, fyi. I suspect ...
Are you saying you have to pump the pedal to get resistance in the pedal so you can get it gear? If so , it sound like an issue with the master or slave. Does the clutch slip when driving?