I'm wondering why the bags didnt line up first time, did you use the Cyclevisions brackets?
My bike is not a Harley. My back fender is a strutless fender. It was a little wider, and shorter than a stock Harley fender. The conversion brackets I used were from eBay. I did end up cutting approx 3" off of them to make them fit. I would imagine if it were a stock softail it would fit like a dream right out of the box.
that bike is.........errr was awesome. your going the wrong way. take the fairings and hard bags off it. lol too each his own but harley or no, that bike is nothing to be ashamed of.