We present the first observations of H$^{13}$CN$(1-0)$, H$^{13}$CO$^+(1-0)$ and SiO$(2-1)$ in NGC,6240, obtained with the IRAM PdBI. Combining a Markov Chain Monte Carlo (MCMC) code with Large Velocity Gradient (LVG) modelling, and with additional data from the literature, we simultaneously fit three gas phases and six molecular species to constrain the physical condition of the molecular gas, including mass$-$luminosity conversion factors. We find $sim10^{10}M_odot$ of dense molecular gas in cold, dense clouds ($T_{rm k}sim10$,K, $n_{{rm H}_2}sim10^6$,cm$^{-3}$) with a volume filling factor $<0.002$, embedded in a shock heated molecular medium ($T_{rm k}sim2000$,K, $n_{{rm H}_2}sim10^{3.6}$,cm$^{-3}$), both surrounded by an extended diffuse phase ($T_{rm k}sim200$,K, $n_{{rm H}_2}sim10^{2.5}$,cm$^{-3}$). We derive a global $alpha_{rm CO}=1.5^{7.1}_{1.1}$ with gas masses $log_{10}left(M / [M_odot]right)=10.1_{10.0}^{10.8}$, dominated by the dense gas. We also find $alpha_{rm HCN} = 32^{89}_{13}$, which traces the cold, dense gas. The [$^{12}$C]/[$^{13}$C] ratio is only slightly elevated ($98^{230}_{65}$), contrary to the very high [CO]/[$^{13}$CO] ratio (300-500) reported in the literature. However, we find very high [HCN]/[H$^{13}$CN] and [HCO$^+$]/[H$^{13}$CO$^+$] abundance ratios $(300^{500}_{200})$ which we attribute to isotope fractionation in the cold, dense clouds.
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