4" of air gaps is a ton of air in the system. It has to be pulling in through somewhere. How large are the areas of fluid between those large air gaps? My guess would be a hose clamp somewhere (master to reservoir or something).
My other suggestion would be to use an a pneumatic brake bleeder like this from HF:
Amazing deals on this Pneumatic Brake Fluid Bleeder at Harbor Freight. Quality tools & low prices.
www.harborfreight.com
I used it to pull all the brake fluid out of my lines during disassembly and it went pretty quick. Put a bottle on the master side, attach that to bleeder valve at the transmission, leave it cracked, and just keep a large bottle of brake fluid at the reservoir for it to pull through. I'd assume a large bottle like what you have would be enough to fill the entire system, plus the extra that you have in there currently so you should get all bubbles out then. Remember to start the air bleeder, then crack the valve; when stopping close the valve before you stop the air bleeder.
But again, I feel the 4" air gaps between fluid seems excessive and it's bleeding in from somewhere else.