I want to generate some addresses using a gieger counter as a random number generator. Lets say I will just manually write down the number of clicks I hear over a certain period of time.

This task has 3 parts (easy I think if you know javascript):

1) Explain where in this script does it describe the random number generation and how it works.

https://github.com/pointbiz/bitaddress.org/blob/master/bitaddress.org.htmlHit ctrl+f, type in ArcFour. Here's the Wiki on it:

http://en.wikipedia.org/wiki/RC4#The_pseudo-random_generation_algorithm_.28PRGA.29It goes around modulo-adding values together, then using the sum as an array key to come up with a new value to modulo-add. It does this a lot.

3) Tell me how long I would need to count clicks for if there was an average of 1 per second and explain the logic behind that.

Depends on how regular the clicks are; i.e. how much variation there is. If the clicks appear 1s apart +- 0.01s with 99% probability, then it's extremely likely that you'll get 3 clicks if you count for 3.5 seconds. You now have very little entropy. However, if it's equally likely that you'll get 1 click or 2 in a 1.5 second period, then you're garnering at least 1 bit of entropy per 1.5s. You'll want as many bits as the algorithm allows.

OR

2) Modify the script so that I can use my own random number

4) Convince me this is idea won't work.

It won't work because I doubt someone will modify the script for you for such a small amount of money. You're better off asking for someone to do it for you for free, or finding someone interested in it. That said, it's probably a simple matter of replacing the mouse-entropy with user-input.