I had the exact problem with the clutch, and it was a bad clutch slave cylinder. Bleeding the clutch was a temporary fix, maybe it is all you need, although if the clutch fluid is gunky, it is probably the slave cylinder. BE SURE TO USE THE CORRECT FLUID (MINERAL OIL RATHER THAN BRAKE FLUID) IF YOU REFILL THE CLUTCH RESERVOIR. Replacing the slave cylinder is a pretty easy fix if you have the part (and the mineral oil). The mineral oil is apparently same as used on some bikes, called "Magura" or something.
I found that the clutch worked almost normally when the bike was cold, and got worse as it heated up. Also, pumping the clutch repeatedly before shifting seemed to help. Finally, I think it also helped if I turned the handlebars all the way to the right and pulled the clutch handle a little bit several times (helps remove air from line?).
Didn't have the symptom with the flashing temp guage--which temp guage are you talking about?