Great project!
Rusted exhaust manifolds was a problem on my 2001 EVC too. When was doing chains past winter, I was not able to remove them and had to move engine forward with downpipe still connected. Luckly, there was sufficient clearance to do that.
As far as rusting on the back side of the crankcase, my original 2001 AXK wasn't that bad. There was some rust, but nothing nearly as dramatic as seen on your pictures! There must be something leaking there in your engine that caused such severe rusting.
Why the plug was blown off in your "good" BDF? With cracked oil pan, I would be very cautious to inspect all internals to make sure it was not ran dry by his previous owner…
-albertr