1997 Honda Prelude Help with transmission

Hello, I have a 1997 Honda Prelude. This prelude was manufactured in 7-1997. It has a automatic transmission that is in bad working conditions. I wanted to replace the automatic transmission but I have read and heard that this transmissions have had many problems and will not hold for a long time if I replace it. Many people have told me that It would me better if I just put on a 5 speed one. But want I want to know is what would I need to do in order to make it work and what will I need to put extra on the car. I was looking at were I need to put the clutch main cylinder on the body of the car. Right near the brake main cylinder, but I don't see the hole where the main cylinder would go into. I was thinking I need it to open the hole myself but I don't know if I should do it. Also I need to change the pedals, but I don't see were the screws will go onto. So can you please help me I would really thank you for your help.