What's the best way to connect pieces of a large print after printing?
Previous answer assuming not yet printed:
If you want to drill holes, print smaller guide holes to guide the drill bit.  The best glue depends on the material.  Printing structures like dovetails makes the connection less dependent on the strength of the glue.
Answer with the parts already printed:
The best way to align drilled holes is probably to glue the pieces together first, then drill the holes.  Otherwise, you need a method to clamp the pieces together or do precision drilling.