Well I pulled the head off today. It wasn't blatantly apparent, but when I looked closely at the gasket surface on the head side, it looked as though some coolant had possibly been seeping across to the pushrod holes. Ignore the really rusty bits on the edges. They're from when the car was parked outside for months getting frosty.
I cleaned everything up and checked the head and block surfaces against a straight edge, and there was no visible variance.
The height of the locating dowels was less than the depth of their corresponding holes. So that wasn't a problem. I honestly think that when I rushed the head onto the short motor the first time, I didn't adequately seal the head bolts and that I was just generally careless.
So I carefully put it all back together with a new head gasket, running a tap down the head bolt holes. I replaced the sump full of milk with a sump full of oil and new oil filter and took it for a drive. I've driven it about 60 kms tonight and touch wood, the oil appears ok. Hopefully no more water gets in the oil.
Just to make sure that my comedy of errors continued, however, when I was fitting the new water pump I snapped one of the bolts due to some crap in the thread and me being a retard. The water pump still seals but I'm gonna have to pull it off again and try an easy-out on that bolt.