making up a rigid frame and welding the manifold to it shouldnt require any specialist work.

It may not be pretty, but as long as it holds the flange rigid to be milled or faced by some means, that's all you need.

The other alternative is to have new flanges cut and weld this onto the manifold after cutting off the warped ones.

That would be DIY'able if you have the inclination and welder

I know a guy who can waterjet you out flanges at a very sensible price