Font Book: Managing Fonts, Duplicates, Warnings etc... Need Help!

How this all started...
I have a lot of fonts. I use them for design purposes, and recently added a bunch of new ones.
As a result, I had a problem with an Adobe program and the font displayed in the workspace.
I figured out which one caused it and deleted it. (I've never used it before, and it wasn't a common font, so I didn't really care).
Problem with that solved.
So I figured that I ought to go through Font Book and check everything else and started Validation (under User).
I had several Errors, Duplicates and Warnings.
I (maybe naively) allowed Font Book to "Resolve Duplicates".
QUESTION 1 (a) (b): Could letting Font Book resolve duplicates create any problems? and how does it decide what to trash?
I also let Font Book move all the Error fonts to my empty Trash Folder.
- I then moved all those to an empty folder on my desktop.
I then moved all the Warning Fonts to another empty folder on my desktop.
So now, in User fonts, there are currently no problem messages.
This is where it gets a little trickier...
In "All Fonts" or "Computer" there are no caution symbols adjacent to any fonts, but if I run Validation, I get a lot of duplicate fonts.
For example... Arial exists in:
Library/fonts
User/Library/fonts
Library/Fonts/Microsoft
QUESTION 2: Do I need to address these? and if so, will that have an effect on any programs that use those fonts?
* I did some research on this, and found an article at Mac World, discussing this, but I don't feel any better/wiser after reading it or the comments...
"Problem" since resolving duplicates and/or moving warning and error fonts (from User):
Since I resolved duplicates, and moved the error and warning fonts, I've noticed some "minor" changes in appearance with websites.
Such as in Hotmail, and a website that I'm a member; the font displayed is now just slightly different.
Albeit, the difference is very subtle, (but as a designer, I noticed this right away) and my concern is how this may affect any design work I do, if somehow the change I'm seeing is more of an error.
* I have to make an assumption that its a font used in scripts (like Arial, Helvetica, etc, etc) that use my fonts for display.
QUESTION 3: So the big question is, how the heck do I address that now???
About the Warning Fonts:
For the most part, the fonts that came up as "minor warnings", showed the message 'kern' table structure and contents.
- I know that "kern" is suppose to be the spacing between characters.
QUESTION 4: So, why does Font Book care and warn about the "table structure and contents" of font spacing between characters, for any font???
QUESTION 4b: If that's NOT what that means, then I'd appreciate a plain English definition (perferably a source from Apple directly).
Caches:
I'm seeing changes on the fly with fonts (and the display on websites), if I try and move fonts that had warnings like Arial styles or Helvetica styles back to my User Directory, so I'm guessing that Font Caching isn't affected by this.
If anyone is going to suggest that I deal with the font cache (since I've read several questions on this topic already), I'd appreciate some explanation about WHY I would need to address font caches and HOW they might be affected in respect to your suggestion and the problems I'm having.
Additional Information:
I use a MacBook, Mac OS X 10.6
~ If there's some other information that you may need from me, then please ask away... I need to figure this out, and Font Book is driving me crazy!!!

Yes hindsight is 20/20. I realize now that I should not have allowed FB to do what it asked. (But that's a moot point now).
Having a large number of fonts is something I've always had for design purposes. I never had issues with fonts on a PC, and didn't expect these sorts of problems on a Mac. And how is someone suppose to know NOT to trust a pre-installed program that's suppose to MANAGE your fonts???
I don't touch the system fonts. I am well aware that they can't be deleted, nor do I add any fonts to that directory.
I agree... I need to narrow down the issue. That was the whole point of posting this!
I do keep backups of my system and files. I have considered just replacing the font folders with what I had before, but it just brings me back to where I had all the warnings, errors and duplicates... And I'm not entirely sure if and how that could affect the font caches, and if I would need to then address those. I've been researching this quite a bit, but so far, all I've found is complaints or questions from people with similar problems. For whatever reason, very few people seem to want to offer help with this kind of problem (but I thank you for at least trying)...
With Dreamweaver, its not quite that simple. If it was, then I wouldn't need the help. Even if we disregard the issue I have with Dreamweaver, the problem also exists on some websites, webmail, etc. Websites (and Dreamweaver) use standard font families and display their fonts from YOUR installed fonts. The font problems I'm have online are not missing fonts, they are just not the same font in size or appearance that they were before (and no, my webmail, and these websites didn't change. I had someone give me some screenshots to confirm). But I can't figure out exactly where the problem is, because it appears that I DO have the standard fonts. It could be that FB removed a version that was better than what was left behind, or it could be something else.... I have no idea anymore. I'm just getting more frustrated.

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<ReportParameter Name="EndDate">
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<Prompt>End Date</Prompt>
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<ReportParameter Name="ObjectName">
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<rd:ReportUnitType>Inch</rd:ReportUnitType>
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Any suggestions would be greatly appreciated. Thanks!

I did some digging and found a link that might help you/have an answer.
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https://connect.microsoft.com/SQLServer/feedback/details/574003/modify-the-default-font-family-for-sql-server-business-intelligence-development-studio-while-creating-a-report#
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Blog:
http://sustaslog.wordpress.com
LinkedIn:
Note: Posts are provided “AS IS” without warranty of any kind, either expressed or implied, including but not limited to the implied warranties of merchantability and/or fitness for a particular purpose.

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      // declare variables
         int array[] = new int[ 5 ]; // declare array named array
         int inputNumbers = 0; // numbers entered
      while( inputNumbers < array.length )
          // prompt for user to input a number
            System.out.print( "Please enter a number: " );
                  int numberInput = input.nextInt();
          // validate the input
             if (numberInput >=10 && numberInput <=100)
                   System.out.println("Number stored.");
                 else
                   System.out.println("Invalid number. Please enter a number within range.");
          // checks to see if this number already exists
                boolean number = false;
          // display array values
          for ( int counter = 0; counter < array.length; counter++ )
             array[ counter ] = numberInput;
          // display array values
             System.out.printf( "%d\n", array[ inputNumbers ] );
               // increment number of entered numbers
            inputNumbers++;
} // end close Array

Yikes, there is a much better way to go about this that is probably within what you have already learned, but since you are a student and this is how you started, let's just concentrate on fixing what you got.
First, as already noted by another poster, your formatting is really bad. Formatting is really important because it makes the code much more readable for you and anyone who comes along to help you or use your code. And I second that posters comment that brackets should always be used, especially for beginner programmers. Unfortunately beginner programmers often get stuck thinking that less lines of code equals better program, this is not true; even though better programmers often use far less lines of code.
                         // validate the input
   if (numberInput >=10 && numberInput <=100)
          System.out.println("Number stored.");
else
               System.out.println("Invalid number. Please enter a number within range."); Note the above as you have it.
                     // validate the input
                     if (numberInput >=10 && numberInput <=100)
                          System.out.println("Number stored.");
                     else
                          System.out.println("Invalid number. Please enter a number within range."); Note how much more readable just correct indentation makes.
                     // validate the input
                     if (numberInput >=10 && numberInput <=100) {
                          System.out.println("Number stored.");
                     else {
                          System.out.println("Invalid number. Please enter a number within range.");
                     } Note how it should be coded for a beginner coder.
Now that it is readable, exam your code and think about what you are doing here. Do you really want to print "Number Stored" before you checked to ensure it is not a dupe? That could lead to some really confused and frustrated users, and since the main user of your program will be your teacher, that could be unhealthy for your GPA.
Since I am not here to do your homework for you, I will just give you some advice, you only need one if statement to do this correctly, you must drop the else and fix the if. I tell you this, because as a former educator i know the first thing running through beginners minds in this situation is to just make the if statement empty, but this is a big no no and even if you do trick it into working your teacher will not be fooled nor impressed and again your GPA will suffer.
As for the rest, you do need a for loop inside your while loop, but not where or how you have it. Inside the while loop the for loop should be used for checking for dupes, not for overwriting every entry in the array as you currently have it set up to do. And certainly not for printing every element of the array each time a new element is added as your comments lead me to suspect you were trying to do, that would get real annoying really fast again resulting in abuse of your GPA. Printing the array should be in its own for loop after the while loop, or even better in its own method.
As for how to check for dupes, well, you obviously at least somewhat understand loops and if statements, thus you have all the tools needed, so where is the problem?
JSG

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13-inch: 2.6GHz
with Retina display
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