Wow, I feel for you..... not trying to be a poster child for Andrew, but the kit I bought from him was spot on and we had no problems with alignment the first time we assembled and ran it. My drive system was different than yours however, and consisted of a complete new set of serp pulleys with an 8 rib dampner.
Oddly, once the engine was rebuilt after the first dyno runs, we encountered misalignment somewhere, although all pulleys showed to be in line with a 1.0m straightedge. After a day of watching the 8 rib belt walking off, and trying to figure out where the misalignment was coming from Dennis simply chucked up a scrap of 6061 billet in his lathe and that soon became a new idler pulley with an outboard flange to keep the belt from walking. Still don't know how the misalignment came about, but we've had to shift the supercharger pulley back about 3mm.