It took a bit of finagling, but I figured it out. Had to do window_frame_set_rect(middleX,middleY,w,h), then window_frame_set_region(0,0,w,h), then window_set_size(w,h), then window_set_position(0,0).
As far as the taskbar overlap, it only shows up on game load, not when player was setting the resolution in game. I just set an alarm on my window manager object with a 20 frame delay that triggers my resolution change script. That puts it back over the taskbar.
Thanks again! Nice to have borderless "fullscreen" windowed be the default but be able to see the frame when it's at lower resolutions. :)