First off, the only way to get air out of the MC is through the banjos or the caliper. The other bolts hold the MC in place.
Procedure without seeing it, like right personal type thing kind of.
Make sure you have fluid in the reservoir and that the hose leading to the MC isn't kinked, this would assure you have fluid available for the MC. Next loosen off one or the other banjo bolts and then pump the MC slowly. You should get fluid in one or two pumps. Don't rush this,the fill hole in the MC isn't a pipeline. Once you have fluid proceed as per previous. If you don't get fluid, remove the reservoir and MC, first to make sure fluid gets to the MC and if that be the case to rebuild the MC, or just thoroughly give it a cleaning. In doing so, if you find that there is corrosion in the MC, rebuild it or replace it. New ones are not available from Yamaha but could be elsewhere.
Post back for more info,,, we don't mind one bit,,,, maybe 2 bits, but not 1 bit.