You are dealing with more aluminum oxide than iron oxide(rust). I would cleaning the engine bay in sections and removing as much as possible to avoid having cleaners and water in areas you don't want them, i.e. the alternator. Also, just moving lines out of the way to make it easier to get to everything will help. I say work in section because you only have about a twenty minute window for removing and treating corrosion. The aluminum parts would benefit from Flitz Aluminum Pre-Clean and mild agitation with scouring pads/brushes. This engine bay is not a one day project if you want it looking new again. So get a game plan together and research how to remove stuff that will benefit from cleaning/polishing out of the engine bay. I would invest in some good masking tape/duck tape to cover things that you don't want sprayed with water and cleaner, like painted surfaces. Removing hardware and cleaning it and removing rust/corrosion would be the best method if you are wanting to replace every nut/bolt/washer that has corrosion on it. DupliColor Rust Fix is a great product for sealing hardware/metal after you have removed the rust as much as possible. [If you don't remove rust it will come back and continue to spread under whatever you spray over it.] DC Rust Fix requires 24 hours curing time before applying a top coat/color coat. You will need plenty of prep solvent and lint free cloths to prep any surfaces that are going to be painted. Prep work is always the most important step to creating any well finished project. To polish and seal any surfaces that are not going to be painted I recommend Flitz Polish which will seal for 6 months in fresh water environments and up to 3 month in salt water. It works on everything from polish metals like chrome, aluminum, and copper, to plastics, fiberglass, and headlights.
Have fun and keep us updated.