There are a few DIY options you could try.

1. Cut it into 3 x 2 port sections and see if that will allow it to clamp straight. Although it may make it worse.

2. Leave as a single piece and bolt it to a spare head or solid chunk of steel. And cut some of the pipes where they meet the flange and re-weld with the flange secured flat.

I definitely wouldnt cut it into 6 separate flanges. Maybe 3 x 2, or 2 x 3 would help a little though.