What has to be done is do not bend or change the tabs on the back of the rail while prepping it. Or the braces going to the rockers. Put the rails against the cross member level with the bottom. Move them out against the rocker braces. then put 5/16 bolts in the rear alignment holes in the rear of the fender well at the hinge area. This pretty much puts the clip where it has to go. Then install the hood and fenders to check alignment. If the braces with the holes coming off of the cowl are damaged or rusted then you will have to do some measuring.
My son is making a fixture to put the 108 cars on for body reassembly. We do enough of them so it will save time if we could put the body and the parts on a fixture then just weld them up. You would not believe how many race cars are out there that are twisted from removal of the fenderwells and they don't brace the rails.
We have one coming from Mike Curcio's race shop in Easton Pa. They cut the braces off to remake headers. They welded them back on with the rear slick flat. Now when you air it up the right front tire comes off the ground. They sent it out the door like that.
