As you've already found, FindWindowLike() returns a list of all open windows of that type, and after a quick test, they are returned in the order of most recently opened to first opened:

Code:

my @window = FindWindowLike(0, "Notepad", "");
print "$_\n" for @window;
[download]

Open one window:

8455346
[download]

2nd window opened:

7931554
8455346
[download]

3rd:

11731214
7931554
8455346
[download]

Differentiating between the windows other than the order they were opened is something I don't have time to review the docs for right now, so you may want to look to see if there are other identifiers or not.