Hey @levelbest,
Yes – it can all be done in Keyboard Maestro.
Use an Activate a Specific Application (do not try to open the Finder like it was a file).
Then use a Select or Show a Menu Item action twice to open two Finder windows.
Etcetera.
However – what you're doing will be smoother and more organic if done with AppleScript.
set winTarget01 to (path to documents folder)
set winTarget02 to (path to downloads folder)
tell application "Finder"
set newWin01 to make new Finder window
tell newWin01
set bounds to {0, 23, 870, 520}
if toolbar visible ≠ true then set toolbar visible to true
set its target to winTarget01
if its current view ≠ list view then set its current view to list view
end tell
set newWin02 to make new Finder window
tell newWin02
set bounds to {0, 521, 870, 1018}
if toolbar visible ≠ true then set toolbar visible to true
set its target to winTarget02
if its current view ≠ list view then set its current view to list view
end tell
set index of newWin01 to 1
end tell
-Chris