Manual to auto question

[Tderuosi]

Hey guys, as I was putting the newly rebuilt 350 and th350 transmission back in my truck today I realized that the tranny was hitting the cross member from the original manual transmission the truck came factory with. This transmission was in there before along with the motor but I do not like that it is rubbing. Is it best to remove this? Are there any issues involved? And what is the best way to go about removing it? They also had the wrong rear crossmember in it for the automatic and I am having trouble finding a parts truck with a factory automatic. Is there anywhere to buy these online or another way to go about it? Any help would be appreciated as I am trying to put the truck back together the right way.