I'm glad to hear the project is progressing nicely.
although you are basically in uncharted territory, I'm thinking your theory about the dipstick is correct. If you are using the 01 oil pan, I'd stick with the 01 dipstick and oil quantities. The part that concerns me is that there'd really be no way that I can think of to ensure that the engine is being properly lubricated in that configuration.. Hopefully there are no other changes inside the engine that allow it to hold more oil up inside the heads, for example.
I suppose there was no way to modify the car to allow for fitment of the 04 pan? I'd like to think that "more oil" is better...