[Chevyrestorerman]

In the first pic you will need to take the low and reverse piston out of the case before cleaning the case. There are three seals on the piston that will need replacing. As far as the holes you refer to most likely they are machined that way from the factory. They may appear something is wrong but are not.
To remove the rear piston you will need to compress the springs and remove the snap ring that holds the spring retainer to the case
Blow air into the reverse apply feed hole and the piston will come out. The seals on the piston become hard over time with the break down of the transmission fluid from heat.