I did indeed capture the VHS video as a reference to aid with the audio synching process. Even with this reference, it's still fairly time consuming to cut out all the 40ms sections that need removing to maintain sync (although it was a lot easier the second time with TESB).
For some reason I got my left and right audio channels switched again - this is with another VCR this time. It must be the audio cable that's wired up incorrectly, unless it's the actual line-in on my motherboard.
I've encoded the video for TESB, but on watching I've noticed that the colour saturation is not constant and needs to be tweaked on the video capped from sides 3 and 4. Which of course means that the 28 hours encoding time has been wasted...