You can if you wish as both are the "A" engines but you won't be changing the displacement. It is my understanding that both the 88" and the 96" have the same bore with the 96" having the longer stroke.
If you are thinking of using the FXD heads, the front FXD head will not have the threaded boss for the top motor mount like the touring models have. Has the boss, just not the hole or threads.