I have just been through this process.
It took 3 weeks at 12 hours per day to convert our Code base since A3.9 8-10 years I think, 75000 lines of code.
I used replacem like the manual said, unless your code is impeccibly layed out it won't do much.
I used textpad replace in multiple files to better effect, but the difference between flags, and the fussyness to upper lower case is what took the time.
If you have a lot of code don't take this lightly it has set me back a month and I've still not got what I had in C-script, only just got the player walking yesterday!
Jethro.