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1- How many functions can you have running at a time, and what are its effects on stuff like framerate
2- How many variables can you make
Both things are system-dependent. The less the better.

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3- for arrays, in the manual, it said something about making sure that the arrays index does not exceed 4 or you'll get an error message....
The manual was probably referring to arrays of size 3. Just to double-check where did you read this? If you define larger arrays, you can use larger indices, e.g. var myArray[50]; myArray[20]=5; is fine..

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4- what are the basic system requirements to run a game...obviously they vary depending on the game....but what do you NEED
Here's the info from our main website:
Minimum: P-75, 32 MB RAM, CD-ROM, sound card, standard VGA card or laptop.
Recommended: P2-350, 64 MB RAM, CD-ROM, Joystick, 3D video card (16+ MB), 3D sound card, Internet access.
Windows 98 / ME / 2000 / XP and DirectX 8.0 or above, and a decent 3D card are required for hardware rendering.

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5- this is more of a computer question than an engine question, how can i find out what my computers stuff are for system requirements, like ghz and all the stuff that effects the game.
You could run dxdiag, which comes with DirectX. It lists a few specs of your system. If you do a search on the net you'll also find dedicated system information utilities.