This is why the car culture is dying.
It's a reasonably big job, but if you want to take it on, do it. People modify cars because they want to, not because it's cheap. If everyone had the attitude of not bothering because it's either too big a job or too expensive then there would be very few "custom" cars on the road.
As above, starting from the engine, flywheel, clutch, gearbox, tail shaft, crossmember(?). You can modify the wiring loom and get the PCM retuned to suit manual, or if you are getting a donor car, use the loom, PCM/BCM/key head from that. Inside the car is the pedal box. You will need the clutch master cylinder and lines.
The easiest way is to find a manual car that is either written off or has a blown engine and use everything from that.