I always shorten the wire on my futaba9550 from the inside. it can be a bit of a pain but it is not that hard. when you open up the servo you will most likely have some waterproofing thich you must very carefully cut and seperate from the board so you can unsolder the wires. once you do that its home free. but remember which wires go where lol.
If your not that confident in doing this i have also seen people cut the servo wire and put new plugs on the wires for the J connector, atleast this way you have a few of chances at getting it right.