You can bundle them and remove the fuse and those circuits will be safe. It was unclear to me intially how installed the new harness is.
Given that update, my recommendation would be to check out the harness before trying to do anything with the engine. Once the harness is checked out and you are confident it is good and safe, then you can do whatever engine tinkering you want without having ti worry/think about it.
If you want some advice/pointers on checking out the new harness, that would be a good topic for a new thread.
