Wow, lots there. First: Look through our old threads.
Second: Never delete an engine. The game has bugs in it that sometimes don't handle deletions well.
In my games, I micro-manage only until I have all double-track. Then I change over to twice-per-year scanning for problems (like empty trains waiting for cargo).
My routes are all set-and-forget (until I see a problem). During recessions I set a few to only half-full, but I also put up with a lot of idle trains. The game has another "feature" that brings the houses within a city into sync with one another, so they tend to produce lots of passengers and mail one month, and then go dry for months (sometimes years). If you see this happen (especially several decades / economic cycles into a map), then you just have to leave trains waiting for the next flood.
I tend to under-serve most routes a little bit so that my trains stay full and making money during average economic times. Except during the initial phase of a game, I resist the urge to buy all of the trains that a boom can fill.
I like my pax and mail to roll fast, so I keep them short. Before the 4-6-2 Pacific, my express trains are only 2 cars. After that, they are 3. Only during boom times with later, more powerful engines do I make some longer (and after the boom, I shorten them back to 3).
When cargo is left at a depot, it continues to age down to its minimum value. I no longer depot pax or mail.
For industrial loads in the complex economy, I mostly have each train work a production sequence (e.g. Sugar -> Food -> [import] -> etc). At the bottom end though, I'll have some heavy, slow trains just pile on something like coal and/or ore to create a ready supply of steel for other, faster trains to transform into goods and autos as needed.
I do set some routes to accumulate cargo through multiple stops (e.g. three wood sources on the way to a mill). These are usually rural, so (on most maps) there's little or no chance for an industry to pop up and intercept my cargo. However, I have been known to do this with villages that supply pax/mail without demanding them (e.g. climb the steep grade out of San Francisco with only a single carload and then add a car to be filled in Reno / Elko / Winnemucca). When those villages grow into towns, such routes are suddenly buggered.