In determining the cost basis of employer stock in an employee directed 401(k) plan with employer stock as an investment, do you have to take into consideration all transactions that affected the participant's account (i.e. contributions, distributions, transfers, loans taken, loan repayments, etc.) or just contributions?

That's a complicated issue. If you want to learn more about this topic, I wrote a very detailed article discussing it. The article is Basis Issues Complicate Qualified Plan Distributions of Employer Securities, 77 Journal of Taxation 334 (1992)