This works here: some large-ish (even when resized) screenshots, so not in line.
Damn, did it the wrong way round (as your screenshot) first time, so here we go again. EDIT: just read your post again, maybe had it correct first time. Which ever way, fixing the window positions in Edit Preferences works.
1. Starting with the default 3 window mode. http://i.imgur.com/JkLmwiN.jpg
2. Detach the tool options and arrange like this. http://i.imgur.com/t8Lo6Yo.jpg
3. Go into single window mode to get this http://i.imgur.com/eSNFX2d.jpg As you found the Tool options are left of the docks.
4. Click-Drag the tool options tab to the hot spot on the extreme right, resize windows to suit. http://i.imgur.com/DajPEQO.jpg
5. Drag layers tab down to start a new group. Add/close tabs to get the required layout http://i.imgur.com/G8SmbNg.jpg
6. Size the windows to suit your computer monitor. Then Edit -> Preferences -> Window Management to save the positions. http://i.imgur.com/H2q3wCR.jpg
..and that keeps those positions on restarting Gimp
I have attached a sessionrc file with those settings. Unzip and put it in your Gimp profile ~/.gimp-2.8/ (rename the existing if you want to save it). Start Gimp up, I kept it small so make any adjustments, save window positions in Preferences.
Damn, did it the wrong way round (as your screenshot) first time, so here we go again. EDIT: just read your post again, maybe had it correct first time. Which ever way, fixing the window positions in Edit Preferences works.
1. Starting with the default 3 window mode. http://i.imgur.com/JkLmwiN.jpg
2. Detach the tool options and arrange like this. http://i.imgur.com/t8Lo6Yo.jpg
3. Go into single window mode to get this http://i.imgur.com/eSNFX2d.jpg As you found the Tool options are left of the docks.
4. Click-Drag the tool options tab to the hot spot on the extreme right, resize windows to suit. http://i.imgur.com/DajPEQO.jpg
5. Drag layers tab down to start a new group. Add/close tabs to get the required layout http://i.imgur.com/G8SmbNg.jpg
6. Size the windows to suit your computer monitor. Then Edit -> Preferences -> Window Management to save the positions. http://i.imgur.com/H2q3wCR.jpg
..and that keeps those positions on restarting Gimp
I have attached a sessionrc file with those settings. Unzip and put it in your Gimp profile ~/.gimp-2.8/ (rename the existing if you want to save it). Start Gimp up, I kept it small so make any adjustments, save window positions in Preferences.