Hello,
For the absence of contacts you can use "No map contact update" in the difficulty setting. It exactly what it does -- remove everything from map outside your ship.
For removing your submarine, you can look into this mod:
http://www.subsim.com/radioroom/down...do=file&id=551
I never tried it personally -- I hate this kind of micromanagement.
For the instruments, I guess you need the sextant (could be screen resolution dependent). I know MaGUI and Ahnarebe GUI already have one. And you need to be sure that SH3 correctly represents stars/sun movement in function of day and time.
Also you probably will need a weather fix -- the stock game suffers from a very long (~week) storms/fogs, making the navigation quite complicated.
But I'm not sure that it will be realistic. On Uboat you have a dedicated officer to track the submarine by it's speed/orientation. So approximate position should be known even without the measurements.
Finally, if you are not experienced, it is probably better to leave contacts on the map. Just to train yourself to take correct measurements -- with contacts you can always cross-check the distances and AOB. Real captains had real proper training.
Hope it helps)