Wil - cheers for your detailed reply.
Initially I thought the creaking, knocking tapping sound was the bottom bracket, but after having stripped the bike down and tried a 105 bottom bracket with 105 cranks, it was exactly the same. Curiously I found that the 107mm 105 bottom bracket fit just fine and when I moved the ring to the inside of the cranks the noise became a lot worse. Inspecting the chain/freewheel it looks like this is just the chainline being off. I put the ring back on the outside and it worked great. I'm running the bike fixed mostly, and the noise is gone, so I guess it's either the chainline or the freewheel.
I rebuilt the bike using the original bits as the 105 cranks are 172.5 (supplied Sugino cranks are 170) which is great using gears but feels too long fixed. I measured the chainline like this at 47mm which surprised me. This is the original configuration I bought the bike in.
I think longer term I'll want to swap the current 42T/16T for something else as I can't spin that fast fixed or SS and blast up all hills no problem. Not sure if I should get a new chainring/chain or freewheel/fixed sprocket.