You can plan the problems out of the C6 to Toploader swap if you are willing to get the parts that make it effortless. A longtail toploader using the car bellhousing is the same length as a C6. It uses the same trans mount location and for the Fairlane, is the same crossmember. There are two yokes for toploaders; the small output uses a C4/28-spline toploader yoke. The big output toploader uses the same 31-spline yoke as the C6. So, if you were to use a long tail big in and out toploader, it is a plug and play C6 swap. The driveshaft needs nothing and everything bolts up.
I did this on my '67 Fairlane. The only issue would be the speedo cable since the C6 uses the driver side cable and the big in and out longtail uses a passenger side cable. Not a big deal.
If you don't have a choice in parts, like one of those weird length early toploaders and using a truck bell, then it's going to be some issues to address.