I kinda miss the hb corridor, but I like the added teleporter in the MH room : looking at the wall and floor that used to be in that spot, it looked like the right spot for an elevator.
I'll start with commented screenshots again.
1) MH room

This wall block highlighted in red is too thin for a player to fit, so I'm not sure a window there would be useful
2) RA /jumppad tube Room
The two levels are now separated - most of the time. If we get too close to the jumppad "tube", we can still render the bottom level without even looking into it. So I suggest again that you try the two vertical portals from this :

Not only will it help in this case, but standing from the outside It'll also spare us rendering the inside of it when we don't see it, thus saving a bit on overdraw.
Regarding the outside : the added horizontal portal does help. But I think that you might want to try adding another one higher...

... for a more progressive transition when we come from lower levels but also for slightly better vis from the MH room..
If we go from the upper level in the shaft "bunker" to the upper RA level, we start seeing the latter room quite early on. There's a small area from which we can see both upper RA and the FULL Mh room :
[lvlshot]http://hemostick.free.fr/quake/q4/method/frommhtop.jpg[/lvlshot]
Highlighted in yellow is the actual gap through which we can see to the RA room (you can enlarge that screenie to see better, although the image is quite lossy).
That's a pretty small gap. I think you can fix this by modifying the L shaped connection between where the screenshot's been taken and the jump pad tube room. You might need axial portals as well.
3)VIS between shotgun and LG
Here's a case where you should use axial portals. As it stands, from either end of that line, looking towards the other weapon, we're processing useless bits of the following room.
From LG to SG :
[lvlshot]http://hemostick.free.fr/quake/q4/method/lgtosg.jpg[/lvlshot]
From SG to LG :
[lvlshot]http://hemostick.free.fr/quake/q4/method/sgtolg.jpg[/lvlshot]
Suggested portal changes :
[lvlshot]http://hemostick.free.fr/quake/q4/method/sgtolgfix.gif[/lvlshot]
The change on the SG side portal should take care of the second issue. However it seems the change on the LG side portal might not be the most effective with the portal in that position. You might have to keep it axial like shown, but maybe move it a little forward inside the YA room. Either way, I'm sure you can sort it out.
4)Back to the MH room
There's quite a bit of overdraw to be gotten rid looking out/in the LG bunker.

Starting with these should help a bunch when we're inside the bunker looking out. Notice the portal on the opening in the higher floor.
You might have to add an extra portal inside the lower level.
Let's pan back to the entire MH room... I still think you should really do the
axial portal I suggested in my first post.
I now think you should also try this out :

-Angle and shrink the big portal to reach that long pillar.
-Add a small portal in the hallway in order to get something roughly equivalent to the original large portal (i.e cuts the entire room, catwalk included).
-Block the remaining "windows".
Finally, I think that overall you might be able to make transitions to big rooms a bit less hard with a bit of func_static grouping of columns of windows. That way each column would pop into view only when it's visible. Might be tricky though, but probably quite a bit useful in the MH room.