After watching a video by Joe Walsh about how to setup a guitar I have started to use a DB meter to set my pickup heights so no matter what pickup I pick it will be the same volume as all the others. I put a set of Fender noiseless in my cheap strat and was surprised by the difference in heights on all 3 pups from the string to the top of the pickup and they are a set and are supposed to be all the same output. If you have a look at a set of Tonerider Generator humbuckers the values are 16K and 8K and while the higher value pup position is opposite from your setup I would say you would be able to adjust the height enough, as long as you have enough adjustment, to get the pickups to sound the same.