I agree with Zamboniman and Bturner2, go with the 120" wide model. It gives you more room when landing and allows you to easily use side guide rails. When using side guide rails, make sure they do not touch your graphics (in my photo above you can see I positioned them slightly below the "MasterCraft" graphics and angled them froward slightly so they don't touch the rear "X2" graphics).
I thought about matching the bunks on my trailer, but it would have been too difficult to fabricate two sets of off-setting bunks. I use a tennis ball hanging from a string to align to a particular point on the boat...this is where I hold it while someone winds the lift up. Everything (including the shaft strut) under the boat clears the horizontal cross member except the prop. I might increase the height of the vertical unistrut that supports the bunks so the prop clears. Then I would not have to be as careful when landing the boat.
I leave the boat uncovered over the weekend (private lake house), but I certainly cover it when I leave. I would never leave my boat uncovered overnight at public dock.
Finally, I ordered my cover with an extra 12" length of valance. This helps a lot with sun and weather. I think if the valance was any longer, it would not look right.