Below loft is a bedroom and that has wet patches on the ceiling. What is causing this?
the problem around the velux is all so causing the other leaks ..they have not fitted the flashing kit correctly .. you need to get them back
I had an old one replaced recently which cost about ?700 incl materials & labour. If you are starting from scratch & the contractors has got to make the hole in the roof to start with I would guess that you could probably add another 50%-75% to that at least
Whoever installed the windows and/or skylight (sounds like a skylight or roof window to me) didn't install them properly. Same goes with the roof. Call back your contractors and have them fix the job.