If this is an informal email, here is another option, "I am sorry for taking so long to reply. I am still working on it. I faced a few unexpected issues, but I'll let you know as soon as it's finished".

Preferred: "I am sorry for taking too long to reply. I am still working on it, because of some issues. I will let you know once it is finished."

another option: "I apologize for the late response. Due to some unforseen issues, I am still working on it. I will let you know once it's finished."