If you're going to go about it like that, then make sure you use AUF's. For example, if you have an unpermutated cube, brute solve using all the PLL's i gave you, and if those don't solve it, apply a U turn, then try again, continue for a total of 3 AUF's.
Here's my configuration algorithms for CubeAssistant. They're just the standard ones I use.
Each case is identified with the following: "Axxxxxxxxx" (9 x's)
x is: (0) Oriented, (1) Rotated...
In the settings there is an option under the Solver/General tab called 'Cancel between phases'. If you just uncheck that, then the solver won't cancel out moves between phases.
I'm not quite sure what you mean by 'weirdly distorted'. Are you talking about the borders around the cubies? They...