Well you can use "treat as one"
The texture is broken into 4 chunks.....
select all 4 faces that you would like.(in red)
then
tick "treat as one" and you can scale the proportions and rotate on the other side of this user box.
Then when you have your settings to your likings
hit apply!!!!!!and your image should have been made to look like "one chunk".
For your flipping problem you can go into that texture edit box and in "Align"(bottom right just under "treat as one") Tick "face" NOT WORLD" this will fix your flipping problem!!! hopw this helps