I beg your pardon, I meant to say that the hood is hitting the intake throttle body.  I have added pictures below, in which I hope you can see my problem.  Also, I have taken pictures of the motor mounts as well for comment.  I used the transmission mount off my parts car but, when looking at it again, it is no different than the original mount for the automatic transmission.  I knew the tranny mount was supposed to be different and assumed, when it bolted up correctly that it must be the right one.  I will search for some pics of the manual transmission mount to compare.