The clutch line has been empty and disconnected for a week while I waited on parts to reinstall. But now that i want to run fluid through the line I can't. When I squeeze the clutch lever, the fluid doesn't get sucked in.
It may just be it's having problem pushing fluid to the slave cylinder.
Were you trying to bleed the clutch line at the time, where you were squeezing the master cylinder and opening the bleed fitting on the slave?
In this case, a vacuum bleeder may be a good thing to buy. They're not expensive and available at most auto stores.
I replaced the slave cylinder on my VFR800 recently and used my MityVac bleeder, and it did an outstanding job. Better than I anticipated.
I expected a few rounds of bleedings to purge any air, but it did it rather quickly.