There are lots of threads on the various topics you raise, so take some time over the weekend to review. Try the homes and mortgages forum also. But in the meantime ...
There will be a stamp duty clawback to cover the difference between the stamp duty he paid (if any) and that which he should have paid as an investor first day. I don't know at what point that becomes payable. Your solicitor should be able to advise.
As regards registering the investment property, you register the tenancy rather than the property. So get your tenant first and sign a lease agreement. Search for a recent thread (1-2 wks ago) on where to find one. Once done, register with
www.prtb.ie within one month.
Regarding tax on income, the
interest your partner pays on his investment property is deductable against the rental income (along with other allowable deductions) and he will only pay tax on the balance. Should not need to worry about it until time to do an annual tax return.
IF his mortgage is relatively low compared to the value of the property, and you already have a mortgage on your now joint property, it may be worth remortgaging the investment property so that most of the interest you are paying together is on the investment property so that you maximise the income tax relief on the rental income.