Nick, there are two drain plugs on the transposing box, the one in the rear is higher than the front one, the level may appear to go down after the first run after re-filling. This is because some gets pumped up into the rear part and stays there, (yep, got me foxed as well). So top up again, there is a small filler plug on top of the speedo drive, a small amount of oil should be put in this.
The small amount of oil relative to the size of the walking beams means that it is hard to drain much out, in your case because of the water immersion it has suffered it might be as well to rock the beams a bit to get any trapped water out. Perhaps a couple of changes with a good run in between, would be a good thing too.
As a good student of HMVF you will know not to use EP oil!
How's your clutch?