Are you talking chassis tweak or spring tweak? If it's spring tweak, then yes you'll want to check the shock towers, if it's chassis tweak the shock towers are probably not the issue.
One thing I find is the motor mount and layshaft screws are very finicky. You want to take your time tightening these screws and make sure all of the screws you use are true and straight. Even if one is slightly off it can cause a tweak like you're describing.
After each run I always loosen off the topdeck, center brace and bulkhead screws and check for tweak on a peice of glass. If I find any at all then I flip the car over and loosen off most of the screws (generally not the servo mount ones) and lay the car back on the glass and make sure it's square. If it is, then I very, very carefully and lightly tighten the top screws, then flip the car and lightly tighten the bottom screws. Note - LIGHTLY - don't torque them down yet. After this I check the tweak one more time and if it's perfectly flat I go ahead and methodically tighten everything back up. Then, check one last time.
The nature of the design leads to tweak unfortunately. I've found my car to tweak after a run even if I didn't tap anything at all. Sometimes the torque from a modified motor can tweak the motor mount. I don't know that you'll ever be able to get a car to run tweak free for a few runs... to me it's just part of my pre-race program.
Keep at it, you'll find a system that works for you. Don't be afraid to experiment with the order you tighten screws or how you do it, you never know when you may stumble on something good. And when you do, come back and share it!
Luke