Clutch reservoir dry - think you've found your original problem.
Okay, the banjo bolt is the bolt holding the clutch line to the master cylinder. Fill the master, pump a few times, hold it almost to the handlebar, then crack open that fitting. 1/4 turn loose and then tight again should do it. Repeat about 5 times and the main bubbles should be gone.
Then crack open your bleeder fitting and pump until most of the air bubbles are gone. Make sure to keep the master topped off. Tighten the bleeder and bleed as normal, 5-7 pumps, hold, crack the bleeder, tighten, repeat until there are NO more bubbles and the handle feels firm.
If it absolutely will not get firm, you may have to get a vacuum bleeder pump like a Mityvac.
If the master was completely dry, I'd highly recommend rebuilding both the master and the slave cylinders. The reason being is that brake fluid crystallizes in the lines when exposed to enough air and/or water and can really gum up the works. You may not even need to buy new seals unless the old ones are cracked or damaged. Also inspect the master plunger and bore and the slave cylinder parts for scoring or pitting. If they are damaged, new seals will just fail, so they need to be in good shape. 90% of the time I only need some parts cleaner and brake fluid to rebuild a hydraulic clutch system. While you have it apart, go ahead and use compressed air to blow any crystals and debris out of the clutch line.