Changing the flags.

Find this section in the revelant startpos file -

//========================================
//Faction Shields
//the filenames of the large and small
//shield images that each faction uses.
//These should be BIF images and stored in
//campmap/shields
//========================================

//faction name, large image name, small image name

Now, I think there's a utility available for editing .bif files, so you could then change the ones you want.

Titles.

I'm not sure about this one, do you mean the special titles, or the governer titles?

The governer titles seem to be in variables.txt in loc/eng, but I can't say for sure.