Terminology:
1) Mechanical Reverse Unit: It is not called an "e-unit". That is a Lionel name for a Lionel product. If it is American Flyer, then the correct name is reverse unit.
2) Transformer lead posts: The AC Gilbert factory did not use the terms "positive" or "neutral". They used the words "variable post", "base post" and "fixed post". The variable post is the AC voltage supplied to the track and is regulated by a throttle. The base post is the common wire and it completes a circuit from the variable post. The fixed post is the terminal with a fixed voltage and is usually used for accessories. They complete a circuit from the fixed post to the base post.
Repair Tips:
1) To service the reverse unit, you will either have to open up the tender or the loco, depending on the year the loco was manufactured. Here is a link to loco wiring diagrams. You can download this and print it off. I keep a copy on a clipboard, along with other info that is useful to me.
http://www.portlines.com/portlinesclinic10.htm
2) American Flyer Repair Manual: Here is a link to an online copy of a common Flyer repair manual:
http://myflyertrains.org/gallery/GilbertFactoryManual
3) Reverse Unit: You can determine if the problem lies with-in the reverse unit or the motor by removing the male end of the jack panel from the female end at the rear of the loco and jumping the leads. Here is a link to a diagram for that:
http://www.trainweb.org/s-trains/diagram/jumper.gif
I'll add other info periodically