Couldn't you just add the data only within your mod itself?
You could add a hash to the block at that area and check for block updates. If any blocks within the hash gets updated than modify the data to fit. You don't need to modify the block itself as the whole system would be done through the mod.
For example you place down a shaft and it detects a portal at it's output side, so it takes the portal block it's facing and finds it's destination, possibly by sending a dummy entity through, and the location of both. Then it saves the co-ords to a table where data can be modified freely.
Whenever you need to do something to the portal blocks in question you just get them from your hash, update the data to the blocks at those coordinates and finally double-check to make sure nothing went wrong.
I suppose a special rotarycraft portal block or being able to use the angular transducer on a portal shaft to reveal the target location would also work too.
