You can see where they've had to extend the runners and thats where most of that grinding is, the rest of it looks pretty good. If I were you, I'd get a tube or two of quick steel and cover the grinding with that to fill it and bring it out level. Then just sand the quick steel back to a nice finish and you're good to go. You MAY be able to use bog, but being in between the extractors it would probably get a bit too hot and burn or fall off, hence quick steel option.
As for the flanges, how much are they out? I couldn't see it being to hard to make some spacers out of some appropriate thickness steel plate. It's not an overly complex shape. Just get some plate, drill two holes with a hole saw the right size, mark around the outer edges of the flange with a scribe, cut out with a grinder and you're good to go. Alternatively, you could just get your extractors skimmed back to suit maybe??
I dont think it would be hard to make the manifold from scratch either. In fact, having just had a look how I would do it, is how I imagine this person did it. Get two of these
http://www2.blackwoods.com.au/infoBANKP ... &P=2024509 then weld up the plenum box with the base plate on top, extend out your runners and weld on flanges. Good to go. But I would stay with the one you've got.
Cheers,