Got the bell housing dust covers in today from Gene:
Notice that hole in the one on the passenger side? That's for the starter. So obviously it's to be put into place while the starter is out, so the starter can go THROUGH that hole to engage the flywheel. Also obvious is I sure as heck didn't want to pull the header off that side of the engine to get to the starter, so I had to improvise. What I did was to cut that dust cover at the lines I marked in red. Fortunately they are only made of plastic, so it was very easy to cut it until I got it to fit. So it doesn't go all the way around the starter, but it certainly will help to keep most of the junk from flying up into the bell housing while I am driving.
And, btw, it takes three bolts total for these things. Two on the passenger side, and one on the driver side. I only got two with them, but fortunately one of the screw, nut, and fastener kits I bought had a bunch of the correctly threaded and sized bolts included.
I kind of doubt that stuff blowing up into the bell housing was causing the drivetrain noise I've been hearing, but at least I feel better knowing those covers are in place now.