Hi Bob
In answer to your question the holes were punched out using a huge steam hammer probably a 70ton model,
Steel had been invented in those days but was unavailable in commercial ammounts as they had not yet invented the blast furnace the steel that they did make was called crucible steel which was very expensive and was used for the hard edges on machine tools.
The Great Eastern at its time was at the cutting edge of industrial knowlage and some of the designs and construction processes were not repeated until the building of the Olympic, Titanic and Britanic in the early 20th century.
Your model is coming on at a fantastic rate of knots I am really looking forward to the launching.
All the best Bob
Paul