You know it wont sound like the duncan in the neck position right? it wont be as thick and should sound a little better actually. If you still want to go about it, the easiest way is to use a push/pull pot to activate the middle pickup. it requires no extra modification to the guitar, control plate, pickguard or stock wiring itself (obviously mounting the duncan does require routing). When you want the middle pickup on you can just pull out the volume pot to activate it.
You can buy the required pot here (quality ALPHA pots)if you cant find one locally:Here you need to choose the value from the drop down menu, I would use 500k Audio considering you are adding a humbucker but if you want to keep the stock value use 250k Audio.
Or you can buy them here too: (far more expensive CTS pots of about the same quality as Alpha's): Here You will want the 5th one or 6th one on this page depending on the value you want.
You can get routing templates from: Here You'll want part numbers 1096 and 1097 for a mustang pickup rout (which as you know fits duncans in it) in a the body and pickguard.
If you want a diagram with a pushpull pot activating the middle pickup I can draw one for you.
