I also have the new 2.25mm stiff lipo chassis and the bulk heads not being parallel does not appear to be an issue, but a good thing to look at.
When i initially built the car the toe was perfect, drove the car, had a few mishaps, the tow was not symmetrical. The same thing happened with an Xray 007. Come to find out if you break a rear arm it puts a lot of stress on the plastic hinge pin holders causing the hole to get deformed throwing off toe.
The nice thing about plastic holders is there cheap, other cars with aluminum holders require a more expensive part to be replace.
I would try the high or low holders in the rear to make sure this is the problem before buying new holders.