Good that at least the ladlady is doing something ... she could have made the registration online to make it faster and give your registration number immediately, but well I guess you can't complain
So you are curently working in Ireland? If yes it is a bit of a grey area since in theory based on EU laws as the spouse of an EU citizen you are automatically entitled to live ad work here; but in practice the document which testifies that you are entiled to that (Stamp 4 GNIB card) takes a few weeks to obtain - and as you have noticed requires a few docuements which are out of your control.
As for entering Ireland and staying here while the application is being processed, I think there is not issue sincwe you are not visa required (I am not familiar with the registration process which you went though, I assume it is for foreign nationals stayig more than a few weeks - but as soon as your EUTR application is in you clearly won't need that anymore).
Anyhow, the only "borderline" thing you might have done is to start employement. But if this was to be escalated I don't think it could really be held agaisnt you as logn as you indeed qualify for an EUR residance card (basically I think they can only refuse it if they have strong evience of sham marriage or that you are a security threat for Ireland).
I wouldn't worry about anthing else ...
And above all I would submit the EUTR application asap. As soon as they receive it your situation will be 100% clear for the next 6 months and your will be allowed to stay and work here with no question and a document to prove it.
Just one thing to keep in mind: they might take up to a month to send back your passport and Stamp 4 letter after receiving your application.