If I'm looking at your wiring setup right I dont think your going to be able to use the battery cover without moving some stuff. It all looks very tidy by the way good job. I also believe the cover is hinged as part of the battery box so you'll have to change the complete box, dont know how much work that would be. Dont think the cover provides much waterproofing, if riding in rain, water could still be forced up under cover from sides but even that is probably not to likely and probably wouldn't cause any problems. I'd say as long as you still have the cover on the positive terminal so it's not likely any thing could cause a ground short to that terminal your good. I'm going to have to see if I can fit my slime compressor under my back seat looks like a great spot but I do already have a tool kit in that area might have to rearrange. Mike