Now that you have the hood off...
It's time to track the source of the smell. Does it smell like burning electrical, plastic, oil or rubber in combination to the usual vacuum smell or does it just smell bad? Usually when there is an issue with the motor you'll have odd sounds in conjunction with a burning smell. It could be something as simple as a worn pulley in that case, or maybe worn brushes or a bad commutator.
If it's not a smell caused by a malfunctioning motor, I'd just strip the machine down and clean it. The motor is very easily removed from the base, the only caveat is that you'll need to get a new motor gasket (which is less than $5), you'll have the best results searching for a motor gasket for a traditional Sanitaire commercial upright since a Sanitaire is basically the same machine. You probably could use a silicone sealant since it works well on a Kirby, so it could work on Eureka/Sanitaire machines as well.
You could wash and sanitize the base and bag after evacuating as much dust as possible with a vacuum or air compressor. I have washed cloth bags in my front load washer (using Persil liquid) with success, I am not sure about top loaders. Hand washing is a must of the bag is vinyl though. For the motor, you could use an air compressor or shop vac to clean most of the dust, while swabbing it down with a (slightly) damp cloth with a cleaning solution. Alcohol wipes work the best, that's what I have used to clean my motors. You won't be able to fully clean a motor, but it is possible to get it as close to clean as possible. I would take the fan off and clean behind the fan as well, since dirt and grime tend to build up behind there (this would be a good time to replace the fan if need be). Do all of that and the smell should be gone. All of my restored machines (three, soon to be four Kirbys, a Royal and a Hoover) have no lingering smells. I would imagine that it would be a LOT harder to remove malodors from a bypass machine than from a simple direct-air machine.