You can fix what you have or go two other routes.
- Install the hard case Yamaha rigging tubes. They look very nice but you'll have to disconnect everything to the motor and then install the cap ends on both sides. By far the nicest but you'll have to ensure that when you raise the motors you don't over stress them. I leaned my engines over (steering to port prior to lifting) and never had an issue. Unfortunately the guys at the marina didn't do this and cracked both.
- Install some zipper type like these. They are a good middle ground to what you have and above. I put the zipper facing down and the material does a very good job protecting the fuel lines and cables. The tight weave doesn't show what is inside either. Finally you don't have to disconnect anything. It's like a zipped jacket that covers what is inside.