Welcome to the forum! 
The shop really didnt do anythign wrong. With a IFS truck there are very few things you can do to lift the truck without spending big money! a leveling kit replaces the keys that the torsion bars go into then that raise the front. For even a four inch lift kit your looking a $1500 for the kit plus instalation! A actual lift kit lowers the front lower control arms to give you a lift plus lifting the rear with blocks or add-a-leafs. You can try cranking up the bars and getting the truck realigned.. However with a leveling kit your truck is actually level. If you raise the bars then youll have to raise the back as well or it will look like its doinf a weelie!
That is real weird that it "suddenly" started to rub. Are your tires low on air? I had to trim my valance and inner fender a good bit to clear my 285's after I raised the bars.