It won't mess anything up, the game is very accommodating of most superficial hacks like that, but it's very easy to spot that it's a fake - as you say, Mewtwo can't be legitimately lower than level 70.
Yes, you can make Mewtwo have all 31 IVs if you want. You just have to make sure to generate a PID for it that matches its nature, IVs and ability. Note that some IV/Nature/Gender/Ability combinations simply don't exist, so you might not be able to get exactly what you want. Pokésav contains a PID generator, or you can use the PID/IV Checker program (download it from this site's main page).
As for "Met at place" - to get this to read correctly for Mewtwo (AFAIK), set it to 3002 - Farawayplace and then change the hex value 46h to C7 and it'll read "Cerulean Cave", where it's normally encountered. And don't put anything in "Egg Hatched"; legendaries can't be eggs.