Guys,
Correct me if I'm wrong but I think the OP wants to change from Major to Minor.
Just in case I understood well here's what you can do...
First of all clone your Midi track. You will need the Major bit for when you modulate (you're not transposing there) to G Major.
So go back to your first track.
Select your MIDI track in Emaj.
Go to PRV - on the left where you have the piano keyboard click on the G# - this will select all your G#s in the whole track.
Nudge down once (from G# down to G)
This will turn your Emaj to Emin.
Obviously you have to repeat these steps for ALL the octaves where you have G# playing.
To transpose to G (relative major of Emin): -
Select the entire second MIDI track which is still in Major.
And in the console view you have a box with Transpose in it.
Input 3
This will transpose from E major to G major.
Delete the overlapping major/minor bits and you're done :)
P.S. Sonar says transpose but in your case, playing a song which start on E min in the verse and changes to G major in the chorus is called Modulation (nothing to do with the modulation wheel on a keyboard).