I'm using the speedway lake header kit and I noticed that the flanges are a little warped in the same spot. I thought it was from welding, but I only tacked the other one and it's a little high in the same spot maybe by a 1/16". Is there to take it down a bit or would the gasket take care of the that
Try bolting or clamping the header flange to a piece of angle iron and heat the area where it is warped. When I make headers I always have the flange bolted to some angle iron or a cylinder head if available.
Did you happen to check the flanges when they arrived to see if they were flat? The higher quality thick flanges usually show up nice and straight, some of the lesser thinner ones could show up not so flat due to manufacturing or shipping. Usually straighten them up in the press. When welding, use TIG and bolt the flange down to a heavy top welding bench or old head. Once you build out away from the flange a bit they usually do not move the flange.
I put a bead of high heat silicon around the gasket ports when I put the header on,and let it dry over night.Fills minor gaps.
I would definitely (as has been mentioned) bolt the flange to an old, extra head then build the headers. Obviously, if this is a 427 SOHC, most won't have a spare head lying around but that is the route I would be taking if an extra head was relatively easy to find. I get that the warp is before welding but I'd hammer the flanges as true as possible, bolt them to the head once straightened, then proceed with header construction.
Those gaskets are great but very thick, sometimes it's hard to bolt them up... You need longer bolts first to compress then shorter for final fit, it can be a pain in the ass.