Re the exhaust housing flange while I would be the first to put my hand up and say that I'm not up to speed with the current crop of turbos used these days from memory the T2's were all interchangeable on that exhaust flange ( and we did plenty of changes )so I don't see why the T25 should be too much different. Perhaps one of the other guys could confirm this.
Re the inlet manifold, have a look at what Sikyne has done with his build. I would be tempted to head down that path rather than using a stock manifold as you will achieve a much better fuel+ air distribution and they are not too difficult to make. Just a bit more tubing required.
All that I can say is that this is what I used both super charged and turbo'd and it worked really well.
Cheers
Dave