What is the ruling on Murabaha sales to a purchaser who orders a specific item, when the company specifies the characteristics and the seller, and then sells it in installments? Is it permissible to set a profit margin?

If you purchase the required equipment and take possession of it, then sell it to the entity that commanded the purchase, there is no harm in that. The specification of the seller or the specifications, or mentioning the profit margin before the contract, does not affect it; because what happens first is a promise, not a binding contract. Increasing the price for installments over the cash price is permissible. It was mentioned in a resolution by the Islamic Fiqh Academy that increasing the deferred price is permissible, for time has a share in the price. Deferred sale differs from usury in that the increase in it is not solely for the deferment, but rather it is in exchange for a commodity, and the Shari'ah does not contradict the nature of things.