From your original question, i assumed we we're talking about a home build costing a few grand, built by you in your
garage/kitchen using second hand parts, not a 400bhp race engine built by the UKs best 1.8t tuner using top end, brand new parts!
A built 400hp motor and a stock AUQ are about as far apart as you can get. Two completely different ends of the spectrum, and little point spending money rebuilding a stock AUQ when those parts would have to be binned if you plan to build something hardcore like that. Same with the vr6, 509hp is obviously with a turbo conversion, so all the parts for that vs a stock one would also be completely different.
I think you need to work out what you are trying to achieve before you spend any money, and if you're gonna be spending upwards of £20k then you could easily buy a newer cupra and mod that to 400hp for way less than a mk1. They have bigger engines, bigger turbos and direct injection as standard.