Hi Trainut!
When I bought my first Zephyr set, off the buy/sell section on this forum, I had no idea of what I was getting into! I was very fortunate in meeting a fellow through the Lionel Collectors Club of America who had been refurbishing both the small and large versions of the cast aluminum sets for a number of years. He informed me of the various part suppliers around, of which several were named in previous posts to you here. But all those suppliers are supplying parts for the aluminum bodied sets. There may be some crossover into the tin sets for wheels or gears, but I have my doubts.
The weak point on the aluminum sets was the cast drive wheels and the 60 tooth idler gear that transfers the power from the motor to the wheels. They tend to swell and crack with age due to zinc impurities in the casting metal.
In your case I think the gear gave out from pushing the weight of the three car bodies. Looking at the picture of your motor again, I suspect your stripped idler gear has its shaft "peened" over to keep it in place. The gear on the aluminum bodied units floats on its shaft, and is kept in place by the gears that are integral to the back of the drive wheels. Your gear may be next to impossible to remove and replace without some machinest work! Plus, the gears on the back of your drive wheels may also be damaged.
I really think you should look for the correct motor to power your units. Used motors do come up on the bay now and then. Or you could get another powered unit and part out the motor.
A good source for prewar American Flyer info and pictures is at Classic Toy Trains forum ( cs.trains.com).-Prewar American Flyer Pictures- an Invitation. Lots of reading about all aspects of AF production.
Picture of my four unit set 
About 50 hours of polishing,rewheeled power car,new exhaust stack,new decals, added grab rails to engineer's compartment door. Runs super nice!
Keep in touch!.......Ken
Good Morning Ken,
Great Train picture, did you use rouge and polishing wheel or hand rub? I am at the moment hand rubbing mine to save the last of the original decals. I don't think I will be able to save them, they keep flaking off. Thank you for good info on the engine.
In reference to paragraph 3 : First a fresh cup of coffee, got it. I have been surfing the web for descriptions and pictures of the zephyr for mine and the engine. I ran across the" BLUE COMET "by american flyer, seems to have the same engine in all detail but as mine has one pick up this engine has 2 pick ups in copper and spoon shape. Does not seem to be cut in half but a likely possibility. Another difference is the reverse switch, again this matches the "BLUE COMET" and if my memory serves me well was made before the 9900 zephyr. Correct me if I am wrong. The wheels on my engine has no inflammation in the wheels but has no hole for a drive rod as yours does and a lot of pictures do on the 9900 1934 version. Must, at the time been using up extra stock.
The idler gear that was on my engine was replaced with a new one sent to me by Harry Henning, thanks again Harry!, was an exact copy. 40 teeth and 7/8" wide and was held in place by the drive wheels, no peening on the shaft. There is a very thin copper washer behind the idle gear, it looks like a small record fitting the shaft and showing some rubbing as being there a long time because, there was harden grease on it and the surrounding area. The gear itself showing on the back a raised shaft between 1/16 to 1/32 inches in rise. To me looks like a zinc gear, not sure or just unpolished steel. The gears again are exactly the same gear. Referencing the drive wheels again, I cleaned them with with warm water and dawn dish soap, both have the usual wear from "the years" thankfully with years left of "great play". Then lined with white lithium. On a first encounter with the axles, they do not remove with out disassembling the frame, lionel had the better idea. American flyer a better built engine with exceptions.
Whew, brain damage from to much thinking. Cobwebs burning, wondering why it was a little warm or is it the coffee?
Referencing transitional/crossover trains paragraph 1: Have a 1201 american flyer (circa 1929 steeple cab {going on memory} maybe "CHICAGO"), uses the above idle gear 60 teeth. The situation I am in, is with the engine on the collector(s). plus a field wire I broke, Oh Joy, Oh Rapture!, Oh .... ! Using a current diagram on the Chicago 1201 supplied by a great dealer! Made to perfection as the diagram showed, but mine had a different configuration on the tabs in my frame. Utilizing what I had left over on my 1201 collector which was not enough. The collector had the pieces of the wire attached to and thru what was the material that held the collector in the frame and a copper tuning fork for the power receptor. I have no idea if it had a roller or a spoon type pick up. All help is need on this!!!!
#33 standard gauge prewar lionel green engine I acquired threw me for a loop. Ran perfect but had no pulling power. Done all kind of surgery, thanks again to Harry Henning and Jeff Kain for parts . Found out what was going on and was told how to rewire the conotator. Great learning experience believe me. Can not remember his name, this has been a while and will have to go back in my notes. It was stated that to look at my engine how it was used in different engines made before mine and the corners where cut on the frame to fit in different newer later models. He had written several books on prewar standard engines. I was informed on quite a lot of issues that needed to be repaired. I had sent pictures of the interior of the engine. To my amazement he stated that he had never seen a standard engine supermotor made that way. Threw him off balance. Seems to be a transitional supermotor probably a "*******" style or experimental. I had no idea because at that time I was just learning about that type of engine.
Have a few more engines like this that make a "Winnie the Pooh day" a new adventure in searching for parts. What I am trying to say is that I lean toward your information ...but it is a possibility the Zephyr could have been created this way?
Thanks for the info and before I bore all of you to death
Trainnut
PS A word to the wise, when working on a lionel vanderbuilt engine please be sure to totally reassemble the engine and shell when testing. Don't leave the draw bars loose and dangling to test a e module, all the time you spent after replacing the barrel and putting it back together will grab the track and throw it off the track onto the table then on to the floor breaking the peg off the barrel inside the e unit. A Winnie the Pooh day, ready for adventure?
