This is very common with replacement windows.
Just go down the edge of the frame with a stanley knife and strip up to the frame. The paper under the pvc will have to stay there
He sounds like an absolute disaster. First get the man from Aqualisa and the other people you contacted to put their findings in writing even if it costs you money. Send a copy of their report together with a list of all damages etc. to the builder stating that if he did not agree in writing to put ...
you did the right thing.
Last time I needed floor joists I went to Jewsons and checked forty lengths of timber before I found 14 that were good enough to give a level floor.
It's the only way.