Absent details, we have to go on assumptions.
First, they didn't kick you out and you still have lots of paygrades left. So, it doesn't appear to be a disciplinary or criminal problem.
Being de-nuked is not the same as if you were never a nuke at all. As much as the Navy thinks it has the power to change reality, the fact is that they cannot go back in time and undo history. You were a nuke, and you are free to say so on your resume. They would be subject to prosecution if they tried to deny it. It is illegal to file a false instrument. In other words, if someone asks if you were a nuke, they have to tell the truth regardless of what NEC shows on your DD214.
So, basically, being de-nuked affects ONLY your naval career, and has little bearing on your civilian prospects. But I caution you to be 100% truthful and forthcoming about it. They can and will deny yu a civilian clearance for lying or for withholding information.
You also say that your command went to bat for you. That is good. It indicates that you could probably use them as references.
If you have no felony convictions, pending court cases, illegal drug use or alcohol abuse that has not been rehabilitated, or associations with known terrorists or anarchists; If you have not tried to commit treason or overthrow the government; If you have no mental illness or psychological condition that affects your ability to work without posing a risk; If you can account for your activities and whereabouts for five years with solid references to back you up, then you should be able to get a clearance.
Civilian licensees are required to conduct (or contract out) their own investigations. They each are responsible for issuing or withholding you unescorted access. If you just cooperate and tell them the truth, you'll have a better chance. Your situation, given the limited amount of information, does not seem hopeless.
Good luck.