... I would like to make a point to him.
And what is the point you'd like to make to him? I think it's a little unfair of him to demand you "scientifically counter" those arguments. This is not really a subject area where science has much to say. He should also understand, as should you, that nothing at that site amounts to a proof, they are merely arguments in favour of disbelief. Some of them are not very good, like #39, which is really just an ad hominem attack on Jesus. Any philosopher or logician would immediately agree that's not a legitimate argument. I haven't read all the arguments, but there's probably at least one more ad hominem attack there, on god as he appears in the Old Testament as a vengeful, murderous, jealous, and generally pretty nasty character. None of that has any bearing on whether god exists or not, so there are probably at least two arguments you can dismiss as illegitimate because they're just ad hominem attacks.
Do you have to give him $250 if you fail to scientifically counter those arguments? And who judges whether you succeed or fail? Him? Not fair, he's not an impartial judge. He's got $250 riding on the outcome, and you can reasonably assume he doesn't want to give it to you. I fear you've accepted a fool's bet. You can't win, and logically neither can he, though he doesn't appear to know that. It is in principle not possible to prove god does not exist, it's only possible to prove he does, and that would require God himself to step in and unequivocally demonstrate his reality in some dramatic fashion. All we can argue about is probabilities.
What I'd do in your position is study up on the common logical fallacies, like the ad hominem argument, the argument from authority, the argument from incredulity, begging the question, stuff like that, and see how many of the arguments at that site you can reject as illegitimate with them. You can find a pretty good list of assorted logical fallacies and explanations here:
http://www.skepdic.com/tilogic.html . Some of them don't apply to this circumstance, but a little reading will soon make it clear to you which ones are useful. And of course you'll have to be careful not to fall into the same traps yourself. You can't, for instance, cite scripture as proof of god's existence, that's an argument from authority and logically unsound.
Good luck, and I hope you can at least have some fun with this.