Your total stat is equal to:
(Starting Stat) + (Stat Growth * Levels Gained * Level Multiplier) * (1 + Level Bonus + Skill Points + Equipment)
Level Bonus = 0.02 per bonus given
Skill Points = 0.03 per skill level
The Level Multiplier is a latent additional multiplier to your growth rate gained for each level that's separate from your level bonus, so characters with faster leveling rates will benefit more than slower leveling characters. Its existance is not well-documented aside from a single line mentioning it on the wiki, as far as I know, but it's quite easy to see if you test it out yourself, even if it can be difficult to measure. However, the thing that's really interesting about it is that its value is different depending on which stat you're looking at. It's also why the actual amount of a stat you gain per level up doesn't match the growth rates (for example, Reimu has a listed SP growth rate of 20, but it only really increases by 2-3 points per level if you have no level bonuses or skill points). If you level a character from 1 to a much higher value in one go, you'll notice that you gain more stats per level the higher you go, even without skill points or any other bonuses. That's the effect of the Level Multiplier.
I can't say I've measured it down exactly, but after running some tests with my higher level files, here are my estimates for the Level Multipliers for each stat:
HP: 1.20 + 0.03 per level
SP: 0.125 (this value never goes up regardless of level)
ATK: 1.10 + 0.02 per level
DEF: 1.10 + 0.02 per level
MAG: 1.10 + 0.02 per level
MND: 1.10 + 0.02 per level
SPD: 0.0225 + 0.000645 per level
It's close, but there's a discrepancy in how the base stat is handled, I think. Using the above formula, assuming I put it into Excel correctly, I calculated out what ought to be Reimu's base level 380 stats (why 380? because this is what she hit with 200 million EXP). The formula gave me values of 57264 HP, 1050 SP, 26361 ATK, 19769 DEF, 29654 MAG, 29653 MND, and 909 SPD.
I then launched TL (3.01) and proceeded to level Reimu on a new game to level 380, assigning no skill points or levelup bonuses. Her stats actually came out at 57446 HP, 1050 SP, 26383 ATK, 19776 DEF, 29669 MAG, 29661 MND, and 915 SPD, for an error of 182 points in HP, 22 in ATK, 7 in DEF, 15 in MAG, 8 in MND and 6 in SPD.
Out of curiosity, I tried the same thing with Marisa (using the same level, though such a parallel wouldn't happen in normal gameplay, to try and pinpoint what was producing this discrepancy). For Marisa, I got predicted stats of 42951 HP/1335 SP/9887 ATK/16475 DEF/42833 MAG/39538 MND/1213 SPD versus actual stats of 43121/1335/9909/16482/42848/39545/1220, for an error of 170 points in HP, 22 in ATK, 7 in DEF, 15 in MAG, 7 in MND and 7 in SPD. Curiously, in spite of the giant difference between Reimu and Marisa's ATK bases and growths, they ended up with exactly the same 22 point discrepancy in ATK.
Finding this odd, I tried running the numbers with Remilia, again level 380. For her, I got predicted stats of 90662/480/52705/32948/13181/29653/1314, and actual stats of 90870/480/51757/32955/13196/29661/1322, for an error of 208 points in HP, -948 in ATK, 7 in DEF, 15 in MAG, 8 in MND and 8 in SPD. All almost the same errors... except for that *huge* ATK discrepancy. Which I'm willing to bet is explained by the fact that Remilia's base ATK is abnormally low relative to her ATK growth.
So, that formula is failing to perform some modification on base stats over the course of adding additional levels which doesn't become remarkably apparent except in the one odd case where the growth rate and base stats don't sync (Remilia). I'm no math expert and can't really claim to know what's missing, though...
