Mustang Trans Match Up
To answer your original question, I have seen many a replacement of a 6Cyl. with a 289/351W. You failed to indicate the year of your Mustang.
Any area you may encounter a problem might in the clearance for the bell housing and the firewall. Later years 289s use a larger bell housing and may cause clearance issues.
The trans cross over shouldn't be any problem in regards to length. Ford used the same C-4 trans on 6 as they did on the 289 with the Mustang. The cross member is the same for all engines/trans combination.
You should use new motor and trans mounts for the 289 and its tranny like you would any rebuild.