I have a probability distibution: $$Pr(n_E) =\frac{1}{4^S}\frac{(2 S)!}{(S-n_E)! (S +n_E)!}$$ To simplfy this into something useful, I take the log of the probability and use Stirling's approximation, which is $$\ln\left[x!\right]\to x\ln\left[x\right] - x$$ when x is sufficiently large. $$\begin{align} \ln\left[Pr(n_E)\right] &= \ln\left[\frac{1}{4^S}\frac{(2 S)!}{(S-n_E)! (S +n_E)!}\right]\\ &=\ln\left[(2S)!\right] - \ln\left[(S-n_E)!\right] - \ln\left[(S+n_E)!\right] - S\ln\left[4\right]\\\\ &\hspace{1cm}\text{Using Sterling's approximation}\\\\ &=\left(\begin{aligned} &2S\ln\left[2S\right] -2S - (S-n_E)\ln\left[S-n_E\right] + (S-n_E)\\ &\hspace{0.5cm} - (S+n_E)\ln\left[S+n_E\right] + (S+n_E) - S\ln\left[4\right] \end{aligned}\right)\\ &=2S\ln\left[2S\right] - (S-n_E)\ln\left[S-n_E\right] - (S+n_E)\ln\left[S+n_E\right] - S\ln\left[4\right] \end{align}$$ However, plotting the probability distribution before and after using Stirling's approximation yields extremely different amplitudes. Why?
Plot before Stirling's approximation
Mathematica Code:
DiscretePlot[ Exp[Log[(2 S)!] - Log[(S - nE)!] - Log[(S + nE)!] - S Log[4]] /. {S -> 100}, {nE, -9, 9}]
Plot after Stirling's approximation
Mathematica Code:
DiscretePlot[Exp[2 S Log[2S] - (S - nE) Log[S - nE] - (S + nE) Log[S + nE] - S Log[4]] /. {S -> 100}, {nE, -9, 9}]
EDIT 1: Updated Graph 2 to corrected algebra and included higher order Stirling approximation: EDIT 2: Fixed @Henry's plot by changing sign of $\ln\left[\pi\right]$ term.
More Accurate Stirling Approximation suggested by @Henry

DiscretePlot[Exp[(2 S + 1/2) Log[S] - (S - nE + 1/2) Log[S - nE] - (S + nE + 1/2) Log[S + nE] - 1/2 Log[\[Pi]] /. {S -> 100}, {nE, -9, 9}]



You seem to have written a partly cancelled
Exp[2 S Log[S] - ... - S Log[4]]rather than an uncancelled version something likeExp[2 S Log[2 S] - ... - S Log[4]]or a cancelled version likeExp[2 S Log[S] - ... ]. But even that will be a poor approximation.You could benefit from a more accurate version of Stirling's approximation such as $$\ln( x!) \approx x\ln( x) - x + \tfrac12\ln(2\pi x)$$
which I think would make your calculation
$$Pr(n_E) =\frac{1}{4^S}\frac{(2 S)!}{(S-n_E)! (S +n_E)!} \\\approx \exp\left[ (2S+\tfrac12)\ln(S)-(S-n_E+\tfrac12)\ln(S-n_E)-(S+n_E+\tfrac12)\ln(S+n_E) -\tfrac12 \ln\left(\pi\right) \right] $$