First off, you need to decide what you are going to keep, and what you plan to discard. Also, keep in mind what you may plan to add later. Ponder that for a minute while staring into your engine bay.
Once you have a clear idea of what you want out this tuck and/or shave, go to the engine bay picture thread and find some pics of something similar to what you want to accomplish.
Once you find a picture of what someone else on this forum has already done, that closely resembles what you want, send that person(s) a private message. We have the technology.
A lot of people have done wire tucks and shaved the engine bay. Everyone has different tastes, abilities, and goals. Everyone does it different. You need to provide adequate information regarding your intentions. There are many levels of what you requested, so you might want to be a little more specific.
See, you never even said anything about shaving your engine bay, but I assumed you were talking about weld-in scottrod panels when you said clean up the engine bay.