I used a product called Superior Aluminum Brightener and it worked great on the gearbox and drivetrain but it darkened the bell housing and engine covers. Surprising given the name but I understand that the metals must be different. 
Any idea if I can vapor blast them back to shiny, or will it take something stronger than that?

I'm a huge fan of vapour blasting, having had three engines and four sets of carburettors done to date. Some of those were very discoloured but came up beautifully. The nice thing about vapur blasting is that it seals the surface and prevents corrision getting easily started again. One of those engines was done over ten years ago and then put into storage. Compared to one done about three years ago, it's difficult to tell them apart.

Got back to working on the bike and had time to cool off. The darkening came off with WD40 and scotchbrite so I think it will be ok after vapor blasting.
I'll be trying Everbrite protectaclear after vapor blasting to hopefully protect the alum even more.