I tack-welded the heater channel in then lowered the body onto the pan. The holes in the pan did not match up with the nuts in the channel. It took all day lifting, measuring, drilling, redrilling....
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Eventually I got all the holes big enough to fit the nuts and washers. Some of the washers had to be ground on one side. But with the nuts all tightened I then put the door on. It closed with a satisfying noise. So I took it off again and lifted the body again. The two chain hoists mounted to the garage ceiling make it easy. Now the body is on sawhorses and I've started welding the whole channel.
One thing I found is that the rear of the channel sticks out too far to get the crossmember in. It will have to be cut back about an inch to get things to fit. I had the pan halves welded in by a body shop. I guess they didn't do anything to ensure the holes would match up with the heater channels. I have two VWs. I welded in new pan halves myself on the other car and the holes matched up perfectly. Maybe I was lucky.
Jason's website mentioned bolting the heater channel to the pan then lowering the body. I don't know how that would work unless I cut out a lot more metal but it's something to think about when I'm ready to put the other side's channel in.