Well, if the engine's got a knock, pull it. I'd probably start with the bottom end. Pull the oil pan and inspect the bearing clearances... depending on how bad it is you may spot it right away.
I highly recommend that you locate amd make good friends with a knowledgable MKIII owner in your area who has done a rebuild before. Forums are great for some types of support, but they're no comparison to having someone who knows exactly what they're doing looking over your shoulder.
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