I would avoid MFT and I think your decision to go with a manual is wise. The MFT and the DCT (auto) seem to be the bulk of the complaints about the Focus. I went with an SE manual but got it "loaded" and couldn't be happier.
If its not grown it's mined!
2013 Ingot Silver Focus SE HB manual, 201a, winter pkg, moonroof. Snorkel delete/K&N drop-in and a bunch of little stuff. Great sticker placement.