Can anyone tell me if there are any programs that can be used to change the clothes of the characters as I wish to make the nameless one look like his mortality at the end and I also want to make fall from grace look like annah in the patch of her

None that I've heard of.
And what you want isn't just changing clothes, but changing sprite models...
AFAIK that's impossible.

Well, it's not impossible to create a new looking character. But it's more work than you would like. First off, you will have to draw animations of the character, like walking, standing, swinging a sword, falling to the gound etc. And that in 8 directions, giving approx. 15 frames in an animation and having 6 or 7 different ways of performing actions, that's over 700 individual frames. Then you would have to put them into a CRE structure and put them in the override directory. You would have to know how to program also then. I haven't heard of anyone crazy enough to do something like that (besides the original designers ofcourse).

To make FFG look like annah might be a bit easier. You would have to hex edit each of the annah files to replace the different ID's of Annah with the FFG ID's. You can use the Inifnity Explorer to find out which ones are used now for FFG. This is dangerous, because one mistake and it all might crash.
Haven't heard of anyone crazy enough to do that either :).