Next...
Your Nexus setting is higher than it needs to be...
It is set at 200, According to the F11 Statistics info it needs to be about 70.
I suggest you change it to 100. Just go into "Map Properties" and change it...
If the game ever doesn't run you will need to increase it...
Always try to keep it just above what the Statictics info shows...

Another thing...
When you build the game...
I wonder what your settings are in the compile dialog.
I find that you can set the "Max Level Size" to 1000.
The default size is 10,000 that is adjustable and only should be what you need.
Simply. lower the number until the game will not compile...
Then increase the setting and compile again.
Keep doing this until the game compiles. Then you have it as low as possable. That will increase the frame rate...

When I run the game from WED I get a constant framerate of about 80 fps...
I have a Sony Vaio with 2 gig of ram and a new awesome Nvidia Video card...
I imagine that your biggest frame rate problem is caused by the computer that you are using...
Although... the wads I am using are all wrong...
I will not be able to test properly till I get copies of your wad files...

I like the moving ceiling fan and the moving doors...
The Secretary at the front dest needs an action. She is running through all of her animation frames.
Therefore, I assume she needs an action attached to her...
That will help the frame rate too...

Also, I am looking forward to running into the ghost...