When MIG welding thin metal, in addition to trying to keep the heat more on the heavier piece you're welding to (sounds like you're doing that), try doing shorter bursts of welds instead of building a typical MIG puddle and carrying it for the length of the seam. And basically walk along the seam that you are welding to build the weld as you go. I've heard some refer to this as "trigger welding". You have to play with it to make sure you're actually penetrating the metal when doing this and not just laying down metal. I've found that if you watch for the glow of the base metal, you can judge the right amount of heat and length of the bursts to get a good weld on thin metal.
Scott
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