Protein-coding genes are transcribed by RNA polymerase II (Pol II) in three sequential stages: initiation, elongation, and termination. During initiation, Pol II cooperates with general transcription factors (GTFs), including TFIIB, TFIID, TFIIE, TFIIF and TFIIH, for DNA binding, promoter melting, transcription start site (TSS) selection, initial RNA synthesis, and the escape of Pol II from the promoter. TSS selection is the step that determines how many and how efficiently TSSs are used, but the selection mechanism is unclear. In Saccharomyces cerevisiae, Pol II finds TSSs through a “scanning” process by which TFIIH’s translocase activity melts the promoter, and the Pol II machinery scans downstream for usable TSSs. Our studies support promoter scanning at all yeast promoters by showing that Pol II mutants alter TSS distributions universally in the stereotypical, polar fashion predicted by scanning models. The role of TFIIH in promoter scanning steps downstream of promoter melting is less well understood. We have proposed a “shooting gallery” model for promoter scanning, where Pol II and TFIIH activities work together to determine the distribution of TSSs and promoter output in yeast. We have identified novel alleles of SSL2 in genetic screens for ssl2 mutants with putative initiation defects. Our screens have identified a number of ssl2 alleles separable into distinct classes based on in vivo growth and transcription phenotypes. We propose that some of these alleles alter promoter scanning in ways that are distinct from how changes to the Pol II active site alter promoter scanning. Our goal is to determine how Pol II and Ssl2/TFIIH work concurrently to promote transcription initiation and influence promoter output.