It would have to be an issue with the driver.. I too am not technical savvy enough to figure how to get it to work. I can tell you that the N64 original controllers use a unique type of joystick function. I've done a lot of searching around on a modding forum, and have found out that they have trouble modding gamecube joysticks into original N64 controllers, but with 3rd party controllers, such as the SuperPad 64, all they have to do is re-wire the gamecube stick onto it, replacing the old one. The 3rd party N64 controllers and gamecube controllers use what are called "pots" on both the x and y axes to transfer the information to main board of the controller. I'm not sure if a modded N64 controller with a gamecube stick in it will work with the adapter, or if it'll have the same issues as the hori mini.
I'm a noob at modding, but I decided I'd give this a try because while it's awesome to use N64 controllers to play with, the analog sticks are annoying in that they wear out and aren't necessarily the most comfortable to play with. I'm starting to do some work on an old super pad 64 of mine, which the joystick broke on anyway. I'm going to buy a used gamecube controller and see if I can rewire it to work inside the superpad. I already cut out the center part of the octagonal shape piece of plastic where the joystick sits in and krazy glued it to the front casing of the controller... I'll keep you guys updated on progress if you're interested. This is pretty interesting stuff.