Are you running a stroker kit? I'm not sure why the crank would be hitting the baffles. It seems that you may have another problem...
I have the Moroso 7 qt pan and I can speak to notching the passenger side k-member. The pan fit fine where is was supposed to be I just took the precaution and removed about 1/8" of material from the k-member to ensure it wouldn't rub when idling.