I will start with the obvious and add as I can with pics etc.
Alignment issues with lowering and the solutions
When lowered the stock arms and links go from flat to inclined. This incline causes the rear to steer abruptly under compression since the toe link is now moving inward as well as upward. The rear LCA is too long to compensate for this quick steering and this results in severe toe in while driving. The combination of toe scrub and the camber contact patch (-2.3 degrees or so) means rapid tire wear on the extreme inner shoulder. Again the wear is CAUSED BY TOE but made worse by camber.
MEGA arms: Will bring in the rear wheel and reduce camber. The result is that the rear arm is now shorter, making it swing in tune with the toe link which is at an angle and causes more rear steering. The result is a suspension that is toe balanced and tends to respond quickly due to the addition of the spherical connection point on the LCA instead of a rubber bushing. The rubber bushing restricts free motion and is an undamped spring force. This causes delay in traction, suspension position and general liveliness of the suspension. Further benefit from aligning the shock body within the spring and sway bar endlink positioning add to the value of the MEGA arm system.
Toe links: Allows the toe to catch up to the camber, pushes the toe link out. The toe link mounting position is moved all the way inward and the toe linkage length is now adjusted for toe settings which changes how the linkage behaves, not just where it sits. It also makes the toe link as long as possible, so it steers less overall. Think of this as making the arc that the link travels on larger, so it moves inward less. If you are happy with a little camber but want to minimize the amount of rear steering and tire wear, then these will do it. They will not adjust camber but help you live with the camber you have. Optimal toe settings on a lowered IS is around + 0.05 to +0.1. NEVER set the rear to negative toe unless you want the car to oversteer over every bump.
The IS300 has a steering linkage that attaches on the back side of the front wheel. When lowering the tendancy is for the car to bump outward (toe out.) This toe change will cause scrubbing and tire wear. To correct this we suggest toe in setting around +0.2-+0.3 for cars lowered 1". This will put the bump curve roughly at center, or make that inadvertant steering less when going over rough terrain. The car will bump out to 0 toe roughly and reduce tire wear.
Front second cause: The rear caster arm bushing is worn and this causes changes in the toe based on road conditions and or suspension play. This is more problematic because an alignment might look good on the rack but as the car travels down the highway it will move in and out of alignment and cause instability and drastic rapid changes in toe. Solution: Front Caster arm #2 bushings from FIGS, then align as above.