How should prices be set when it is difficult to determine the actual cost of production?

Price and cost are independent (think of supply and demand). Price will be determined by the market. If an item sells for $100, it will sell at $100 regardless of whether the cost to produce was $10 or $99. The question is whether or not you will produce that product at the available profit margin. If the costs are difficult to determine, that means there is some additional risk involved. A riskier product requires a higher return. So compare the projected market price to the expected value of the production costs to see if the return is sufficient to warrant the risk.