Can anyone explain how to change the position permanantly for all airports
You can't, and you should't, because every airport and every gate is different. Have you read the explanation at pages 33-34 of the GSX manual, about how the stop position is calculated ?
Also when the jetway comes to the L2 door, it does not quiet line up, as the jetway seems to be about .5 of a metre to low.
It's not very clear what do you mean with "the jetway". A jetway of a default airport ? If yes, it's totally unrelated to GSX, and the only think that controls it, is the aircraft.cfg file.
A jetway of a 3rd party airport that uses SODE, instead, use the GSX door configuration, provided you call it from the GSX menu, not the SODE menu (in that case, it's affected by the SODE airplane config).