Before you finalize, check in with Wynne Windows installation instructions. Rather than 1/8" thick foam, I believe they recommend a polysulfide caulk (can be removed later) ... apply the caulk, install the windows, tighten to 'close' to final tightness, clean up any squeeze-out, let cure, then finish tightening. This may resolve the screw length issue. In any case, explore around a bit on how clamp-in windows get installed ... I'd call Wynne tech support to verify what I say (I might be wrong on which company suggested installing this way).