Wow....Lots of questions. I do a Flyer repair column in the S Gaugian magazine. Tom Barker was the original writer of the Roundhouse Column. It is my opinion that all the engines you are operating need a complete tune up and cleaning. Gilbert engines in good running condition do not show the problems you are writing about. Now, not being able to see the engines the one complicating factor is are there ware issues. Being produced in the 1940's and 50's wear could be a factor.
Flyer Pacifics all have the same chassis and motor. A smoke-in-tender is a different animal of course. The blind driving wheels of all these engines do not touch the tracks. The same is true for the Northern. The Northern could possibly have the later larger motor which means it could pull several times the 6 cars.
None of the engines should slow down as they run. The 350's noise is not normal. Your S-I-T smoke problem is not typical if the unit is completely rebuilt. Follow Tom's books on that or the online repair guide at the Port Lines Hobbies website.
One thing I would note is that Fastrack was not designed for these engines. It was designed for new Flyonel engines. I suggest Gilbert track could be a better option.