Some time ago, I read an article in The Times about self-directed individual retirement accounts invested in stocks. The Times noted that it is difficult to match the dollars in an account with actual stock purchases. When I read your original article I thought the problems you cited could be avoided. I was wrong.
I started a small self-directed IRA with the financial arm of a well-known savings and loan association that works with a brokerage. In doing so, I had to give them permission to add and subtract from the account. That is where the trouble began.
Unauthorized transactions became evident: taking money from the account with no explanation (took six months to get it back); unauthorized trading--two short sales on the statement (when short selling is prohibited in an IRA); with a stop-loss order of $9.375, 300 shares of stock were sold at $9.50, at the absolute low in the trading day (took three months to get the stock reinstated).
If I hadn't kept a close watch on all transactions, the loss might have been considerable.
Since I am over age 59 1/2, closing the account should have been simple. No, my last statement included charges of $45 as a "delivery fee" for furnishing three companies' stock certificates. They have assured me that this matter, like all the others, will be taken care of and "We are sorry, Mr. Haas." This reader has learned a lesson on self-directed IRAs.