Hi,
Legal and beneficial ownership can be separate entities for rental purposes.
It would be acceptable if the monies were paid into a joint bank account as HMRC will recognise the beneficial ownership split from a valid declaration of trust.
You are correct with regards to the mortgage interest. The person who holds the mortgage can only claim the interest portion as a residential finance cost.
Stamp duty is not dealt with on this forum. You should call their helpline on 0300 200 3510.
I have attached a copy of the stamp duty manual below, this may answer your question without calling their helpline.
HMRC cannot comment on remortgaging. You will need to obtain legal advice on that matter.
Links below to your questions should help:
TSEM9800
Stamp Duty Land Tax Manual
Thankyou.