Icecold, that redirection run line worked! The Boinc2 shortcut pulled up the Boinc2 folder tasks. I am uploading those saved / completed tasks now.Copy and run this in a run box(windows key + r if you don't already have it enabled):
"c:\Program Files\BOINC\boinc.exe" --allow_multiple_clients --redirectio --detach_console --gui_rpc_port 31418 --dir C:\ProgramData\BOINC2
and then let me know if your BOINC instance 2 shortcut works.
I assume I will have to modify the line to point to the Boinc3 instance.