1) If you do not exceed the threshold in a continuous 12 month period then you would not have been obliged to register. However if you now see that average monthly sales are such that you would definitely exceed then you should register from now anyway regardless of any issue on the initial period.
2) & 3 ) You have supplied them with invoices charging VAT illegally. They are not entitled to VAT input on them and if they have claimed VAT on them and are audited by Revenue they wil be disallowed. Of course they should not have claimed VAT on them once no number on but many businesses overlook that innocently.
You could retrospectively register from the start, you would owe the VAT but your clients would be entitled to the VAT input credit. You would also be entitled then to claim VAT on your costs in the period. However you can only register back when over the threshold. i.e. If registering while under the threshold you can only do so from the current period.
If you should have registered and do not, when your accounts are filed with Income Tax that may result in a VAT registration enquiry.
You need to work out the position so far, see where you stand vis a vis the threshold. I also urge you to engage the services of an appropriately qualified person, accountant/bookkeeper to put this in order for you.