What is the ruling on financing a supermarket for an orphanage by means of purchasing goods and paying their value to the merchant, then selling them to the owner in installments over 3 years with a 6% profit and 0.4% stamp duty?

What you mentioned is impermissible because it is an interest-bearing loan, not a Murabahah (cost-plus-profit sale). For it to be permissible, the institution must truly own the commodity before selling it to you, and be responsible for it. Then, you would buy it from them at a known price that is not subject to increase if payment is delayed.