Let me preface this comment with the caveat that I'm am in no way an engine builder nor have I played one on tv. I have stayed at a Holiday Inn but it's been a long time.
If they are bottomed out in the case and they are sticking up this much then I'd just get shorter case studs. There could be a couple reasons: They may have been packaged wrong and they're longer than expected, the person you ordered them from gave you the wrong size, or maybe the case was drilled shallower than your previous one. either way I'd just get shorter studs.