Worked a few days before work visa approval after graduation

Hi everyone,
I was an international student in Japan and I’m really anxious, so I’d appreciate any experiences or insights.

Situation:
• I was on a Student (留学) visa
• Graduated from university on Sept 10
• Applied for a Work visa (Engineer/Specialist in Humanities) before graduation
• The work visa was approved around mid-September

Problem:
Between Sept 11–16, before my work visa was officially approved, I worked 3 days at my future employer (about full-day shifts).
At the time, both my company and I mistakenly thought part-time work was still allowed because:
• I still held a student visa
• I had just graduated
• The visa change was already in process

I now understand that after graduation, student-visa-based work is no longer allowed, even part-time.
I am in process of naturalization
• Consulted an immigration lawyer and lawyer told me to report it to immigration
• Prepared a personal explanation letter
• Company prepared an official explanation letter taking responsibility
• Planning to voluntarily report this to Immigration before submitting my naturalization-related documents

My questions:
1. Has anyone experienced something similar (working briefly between graduation and visa approval)?
2. In practice, how strict is Immigration in cases like this when it’s voluntarily disclosed?
3. Is visa cancellation or deportation realistic for a short, first-time mistake like this?
4. Any advice on what not to say or do when visiting Immigration?

I’m really stressed and losing sleep over this, so any real experiences or calm advice would help a lot.
Thank you.