How does the "face import patch work"?
Make sure the latest patch is installed. Import you ME2 character.
How you get your original Shep?
As per this convenient guide and my own experience to corroborate (bolding and grammar correction is mine):
During character creation stage, select the "Import ME2 Character" option to import your Mass Effect 2 character into Mass Effect 3...
You CANNOT import Mass Effect 1 files directly into Mass Effect 3. You can only use Mass Effect 2 characters.
Also note, that based on Shepard's actions and decisions in Mass Effect 2, there is a chance that Shepard died in ME2 and did not survive. If in your save game Shepard is dead, you will NOT be able to import Shepard into ME3.
After you have imported Shepard from Mass Effect 2, you will be allowed to make changes to Shepard's appearance...
You will also be allowed to change Shepard's class at this stage.
More info on what imports on the wiki.
You should note that "ME3 does support cloud saving for new or imported ME2 saves, but it does not support importing endgame saves directly from the cloud." as per the tutorial
Do you need to start a new game with the import or can you use the end-game import?
You need to start a new game with the import. Endgame import does not allow you to append in ME2 save data information. I don not believe it even takes you back to the character creation stage to find such an option.
What will you lose by starting over with an imported save?
You won't lose your achievements for restarting. You can have all your achievements reset on this game on your 360, but in this case it wouldn't be because you restarted as it is apparently some sort of Origin shenanigans.
I'm not sure which perks you're referring to, but if it was anything related to level, powers, reputation, weapons, armor, mods, credits or bonus power, then those aren't going to carry over as that information is going to be pulled from the ME2 save. So your perks will be lost.