If you haven't heard of this program:
http://www.ticalc.org/pub/84plusce/asm/programs/faster.zip

It'll actually make any 84 PCE up to 30% faster, and yes, it does work, with up to a 31% speed gain in my testing against a stock 84 PCE.

Since even still, the TI-84 Plus CE does graph slower then an 83/84 Plus monochrome calc, I'm wondering how I can make the program "permanently" run, so whenever I turn on my calculator, it auto starts, since this program does make it around the same speed of a default 83/84 Plus graphing calc.

Here's what the readme says about the program:
The speed boost comes from changing the wait-states setting for the flash.
The calculator's CPU actually runs fairly fast for a Z80-compatible CPU, but the
OS is located in flash memory (which also contains your archive space), and all
code executing there is severely hobbled by a 9 wait-state penalty, reducing the
effective clock speed by nearly a factor of 10. This program decreases the
wait-states to 6. (The hardware allows a minimum of 5, but that crashes my
calculator. 4 should work according to the flash chip's datasheet, but only if
you make some assumptions about signal hold times and TI's designed bus topology
which are apparently not true.)

Anyways, suggestions anyone?

You have two available methods, neither of which are great.

1) Create an combination of the OFFSCPRT AppVar and a raw getkey hook that executes this program when the calculator is started. Or use ONSCRPT, noting the subtle differences.

2) Patch the OS to look for the program on load, and then run it if it exists. This isn't recommended unless you feel confident in what you are doing.

Other than that, there is really no way to have the program start on boot. Hope this provides more information on this topic!

Is "Detect Asymptotes" off on the Format menu? I've noticed a significant speed gain (to the point where Simultaneous graphing becomes feasible!), so I'd recommend measuring speed differences with "Detect Asymptotes" off (If you haven't already done so).