Thanks for your question
In your favour it may well be that had you paid yourself a part wage - that this would have not given rise to tax but to some Class 1 employee (and Employer) National Insurance.
But yes you should have been completing self assessment and whether you do this now or await the instruction from HMRC through their compliance check this will not later how HMRC view this enquiry.
1 would be inclined to wait - because if there is no tax or National Insurance position arising, you can then just argue the fact that
1) as there was no tax liability arising - you did not realise that self assessment was required - (or that National Ihnsurance would arise) and this was on the basis that
2) You followed suit with what your accountant had undertaken for you
The sticky bit in this - is the fact that a salary was paid in 2013/2014 for £7488 - and I am afraid arguing that you thought HMRC would bill this for you - will not be accepted as you were submitting company information not employee information, or you as a director style information.
But Can you advsie what you mean when you are concerned that HMRC might widen the search? Do you mean going all the way back to when you first started this company?
And how did you live on £5000 a year when you advsie thats all your took from the company (or at least what you declared) IF you genuinely only took this out then do not declare a wage that doesn't exist - you are making matters worse than they are.
I fear HMRC are going to expand their search whatever you do or dont submit now, but any submission you make now will be seen to cover tracks - so will worsen the situation for you
MY expert advsie, let them review the position - be honest that you have made mistakes when they present them to you and ask how to rectify the position.
If they accept its a genuine mistake - then the penalties will be low - if they find its deliberate then the penalties will be higher - but if you have taken money from the company other than the dividends then unless below the 20% threshold in combined income and less than the tax and National Insurance limit generally then there will be these to pay plus interest and penalties
Let me know if I can assist further