The locking collar and the inner race of the bearing are still there as you suspect. A cutting torch will take those both off easily, but if you don't have one, a propane, preferably a MAP gas torch can be used to heat both pieces to a orange, red color, then cooled to loosen them up to beat off with a hammer.
Sand the shaft to remove burrs. A socket or pipe of the diameter of the inside race is proper to tap the new bearings on to the shaft. Yes, replace both bearings. There appears to by a snap ring or something beyond the bearing race. The book doesn't show anything AND it doesn't show a seal. There should be a seal in the case to keep the grease in and dirt out. I don't see one, so the tolerance between the shaft and housing should be very close and no wear at this point.
The "dust" in the chaincase is not a good thing and indicates that the grease leaked out. At this point, clean the case, chain and sprockets thoroughly then use corn head grease, such as Tractor Supply Super S #00 Cotton Picker Spindle Grease