The problem with the auto's under that much power seems to be that the front diffs tend to fail before anything else. The fully built trans can handle it, and the diff handles it for awhile, but over time, the stress, especially if the car is being used at the strip, takes it's toll. A built auto with a higher geared final drive would make a big difference since there are less teeth on the pinion gear which means each tooth is thicker, meaning it can withstand more torque, stress, etc. (4.44)
Other than that, the best option really seems to be a 6 spd. After all, the Shadow Machine has held up over quite awhile now in all different circumstances, and has never been treated "nicely"