I find that the Limits for most of the arrays in the Database for VX Ace are sufficient, but I need to increase the Limits for the Troop array and the Enemy array.

999 is just not enough for either Enemies or Troops, I am using 30 troops per region on average and that limits me to around 33 different regions inhabited by enemy groups throughout my whole game when I need around 100. That is not nearly enough, I would like to make the limit at least 3000 maybe 5000 and I wish to change the enemy amount to 2000 as well.

I have been looking through the Script editor and have had no luck with this, does anyone know where this can be changed, perhaps it is because there is only one line of code that controls all max array sizes throughout the entire Database and not individual ones.

There is no limit on the database side. It's a limit imposed by the editor.
Well, specifically, they limit how high you can set the limit, but they don't actually put a limit on how many elements can be stored in the array, so if you have 5000 items, it will go ahead and display all of them.

You can use this: http://rmrk.net/index.php?topic=45210.0

Remember to CLOSE your project and then OPEN it again after it's finished because it's rewriting your rvdata2 files.
Better back-up your data as well since it doesn't do it for you. Some people have lost months worth of projects as a result.