Just get used to AutoHotKey or AutoIt. Learn to program your mouse behavior via that scripting engine.
It involves mouse behaviors like moving, clicking, dragging, etc.
Give your monitor size information, position/coordination of your skills (either the listed menu (with scroll function), or overall view of all skills (pointers)), let it click them, point to the new skilltree-window of that respective skill, let it click a desired node (info: you don't have to click each skill node at once, just one which you want works too, sets the path immediately, BnS does itself), apply it, done.
Assign a key for it, you are ready to go.
Besides, whats so difficult by changing 1-4 skills manually ...