TPM has a good article on some of the loopholes that could have been exploited, and also links to a more technical discussion of some possibilities, revolving around the UBIT (Unrelated Business Income Tax) on pages 40-48.
His 401(k) could simply be a self-directed investment account. I have one that is a Roth IRA. You are limited in what can be deposited into the account, but it can grow without limit from capital gains.
Aren't the contribution limits on IRAs only referring to the tax deductible portion? I thought you could contribute after-tax dollars without a limit.