personally i would leave the old lid in place and screw it air tight ( or run a bead of silacone around it then screw it on )
the new outlet for the pipe is easy to do, jsut get a TANK connection kit from a plumbing center
the hole to fill with, well i would just get another tank connection kit ( this time the biggest you can get, 1" could be the biggest and connect a upstand of some pipe to that with a end cap on it, that would stop it slopping around and up and out the pipe,