Comma use and "that" vs. "which"

I've been proofreading my friend's novel and the experience has left me very confused. I'm a native Spanish speaker, and maybe that's causing interference in my English. But anyway, if anyone could help me with the following on comma uses, it'd be great. Any elaboration on rules is welcome.

1) John gave him this, so he could finish.
or
2) John gave him this so he could finish.

1) Jeremy came to the new theatre on Bourbon street because he wanted to finish the movie.
or
2) Jeremy came to the new theatre on Bourbon street, because he wanted to finish the movie.

1) Henry, Tom, and Dick went to the movies. (I was taught this way in high school)
or
2) Henry, Tom and Dick went to the movies. (I was taught this by a journalism teacher)

1) John gave this to him, but not to Henry.
or
2) John gave this to him but not to Henry.

1) John gave this, but not that.
or
2) John gave this but not that.

1) John gave this, but stole it back.
or
2) John gave this but stole it back.

Finally, my most confusing question deals with the use of "that" and "which":

1) There were trucks in the warehouses, which James bought with his fortune.

Does that comma make "which" grammatically refer to "warehouse" or to "trucks"? I noticed that my grammarcheck on Microsoft Word would highlight it as wrong if I'd write "warehouses which". I'd the "which" to refer to "trucks" in this case. If I use "that" in the original sentence, I'd assume that what James bought were the warehouses, not the trucks.

Thanks for any help.