Forced alignment is a popular technique for gaining phone-level audio transcriptions, but the pronunciation dictionaries used by it are typically based on standard varieties of US English, leading to errorful outputs for non-standard varieties. We employ a customized pronunciation dictionary with the Montreal Forced Aligner to increase labeling accuracy of the prenasal merger (a.k.a. pin-pen merger) in Southern US English. We allow the aligner to choose between IH (/ɪ/) and EH (/ɛ/) in words where the merger is expected, rather than enforcing a standard, unmerged pronunciation. We examine the tokens reclassified from EH to IH when using the new dictionary, and we use formant values to study the acoustic separation (measured by Pillai scores and Euclidean distances between centroids) between vowel formant clusters. When applied to the Digital Archive of Southern Speech (DASS), we find that the modification increases the separation between the prenasal allophones of IH and EH, and also that the proportion of prenasal EH tokens reclassified to IH is correlated with the original degree of separation between prenasal IH and EH for each DASS speaker. K-means clustering is also used to show the modification yields more accurate phonetic transcriptions, measured by increased precision and recall.