Here is a fast primer on how a MC works. Parts are left out that you should already know. Ignore the caliper as the piston just sitts there imperceptably moving.
There are two holes in the bottom of the reservoir leading to the bore of the MC. The larger hole is feed hole for the back of the piston seal. The extremely tiny hole is in front (closer to the exit) of the piston seal.
As the brake is depressed, the rear, larger hole feeds fluid to the back of the piston. The tiny hole is just in front of the lip of the seal and gets covered as soon as the piston moves.
Releasing the brake has fluid behind the piston seal moving back into the reservoir and feeding around the edges of the seal to make up any volume change from pad wear. The tiny hole gets uncovered when the piston is all the way back. This is extremely important because the heat built up from braking will expand the fluid and the tiny hole is the only way for the pressure to be relieved.
If the holes are blocked the piston cannot move freely. If the tiny hole is blocked, the brake will eventually lock while the bike is moving.
The internal MC spring is what moves the piston and seal back into position.
Air is usually trapped in the system when it is rebuilt and is a bear to remove. I remember my friend, a great amature mechanic, having problems bleeding the air from his Ducati. He mentioned the lever eventually got hard as all the air bled out over time. The trapped air had to come out from the tiny little bleed hole in the MC. After repairing my brakes I need to tap on the system and watch tiny bubbles come out of the little MC hole. Back disk brakes are the worst to bleed.
Check the MC holes to be sure they are clear. If you need to take the MC apart make sure the piston and seals move freely enough for the spring to over come the friction.
Tom