I've fixed your totodile for you, the Special Def has to be a multiple of 8 and the nature you want has to be in the Type1 section of your PID Generator. So I made it the lowest I could while retaining it's gender. As for the evolution. Stats are calculated after the pokemon levels, so I believe you are able to level it to whatever level and simply change it into it's next evolution. The game will change it's base stats by itself, so don't mess with those, and the stats will even out.
mytotodile.pkm