I'm very surprised ford have supplied a stat housing without the pipes shown already in it, but maybe that is how they do it ?
With your old housing being scrap now due to the hole in it no doubt from media blasting you have nothing to lose by taking the pipes out of it and putting them in the new one, but need to use some decent sealant around them when fitting, like loctite 5900 or 5910.
I would first double check with either ford technical or the workshop foreman if it is correctly supplied in this state first.
tabetha