Just so we're clear, it's not a matter of making a manual transmission out of an automatic. The process is to replace the automatic transmission with a manual transmission.

You'll need the following from a from a manual-trans Integra:
* Pedal assembly
* Clutch master cylinder
* Clutch slave cylinder and hydraulic lines
* Manual transmission (obviously)
* Interior shifter console
* Shifter linkage and base plate.

As far as the process goes, I would strongly recommend you buy a set of the HELMS factory service manual for your model year. The diagrams and instructions for removing the various bits you won't be reusing are worth the cost of the manual alone.

Lastly, a practical question to ponder.
How old is the car and how many miles are on the motor?
If it's truly at the end of it's life, it would probably be easier and cheaper to sell the car and purchase a manual-trans Integra instead.