The upgraded HPFP includes a larger piston so that it can flow more fuel - so its an upgrade as such. From memory i believe it allows the HPFP to flow around 40% more fuel. I installed the Autotech HPFP upgrade on my Golf R (and did a comprehensive DIY) and never had an issue, so either your pump was worn or perhaps you have pinched one of the o rings and this is causing the leak.
Autotech HPFP Upgrade full DIY guide with pics
As for the fuel in your sump, personally i would drain it and refill with just some cheapish oil and run that for a day or two. Then flush again and refill with your normal oil. The engine flush products that you add to the oil, and let the engine run for 10-15 mins before draining are designed to remove sludge and gum/varnish from oil galleries etc - personally i think a flush product would be useless in this situation.
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