Aye, the Kernel taproom was closed down a good while ago now as they didn't feel they could safely handle the numbers turning up. The mile is pretty good fun but can be overrun with twats who clearly don't care about the quality of the beer and whinge relentlessly about the fact the most of the breweries don't serve pints.
In practical terms, if you're planning to include Fourpure (and I would recommend you do), then I'd suggest starting out there as it's a fair distance from everywhere else, heading back via Partizan, Brew By Numbers, The Bottle Shop, Anspach & Hobday, and if you like cask (which I don't, but horses for courses), Southwark. You're then at the biggest cluster of breweries/toilets and also nearest London Bridge for when things wind down.
Anspach & Hobday are doing some sort of Oktoberfest special this weekend, was planning to head down there Saturday afternoon.