I would pull the clutch cover back off, and make sure the actuator arm is lined up correctly, and everything else is correct. With the bolts that small (8mm, right?) you always want to use a 1/4 inch drive ratchet, and the shorter the better. No need for a long ratchet or excessive force for such small bolts, especially on the motor. Hopefully the stud comes out as easy as it did last time! Good luck.
THE 80's RAGE! Currently owns:
81, 85 Yamaha Tri Moto 125
83 Yamaha Tri Moto 200 x2
82,83 Yamaha Tri Moto 175 project
85 Yamaha Tri Z 250
84 Kawasaki Tecate 250
84 Honda ATC 70
85 Honda ATC 350X
84 Honda ATC 250R
(2) 84 Honda ATC 200x
82, 83 Honda ATC 185s
81 ATC 200
Lots of other parts and bikes