MacBook – 1TB ssd in late 2013 rMBP 2.4 i5

4GB of RAM isn't much to be running all of those heavyweight apps at the same time. My guess would be that it's doing a lot of paging to disk. Check the size of the swap files on both machines.

1. Go to the Finder's "Go" menu and select "Go to Folder…".
2. Enter /private/var/vm/ into the box and press the "OK" button.
3. Add up the sizes of the swap files.

If it's more than 1GB I usually reboot. That will clear out these files. I've seen these files up to 4GB on a machine with 8GB of RAM.

Since running out of RAM can cause writes to disk, the difference in disk speed may be what's causing the delay.

3 external displays DOES work.

I am on a Late 2013 MacBook Pro. I have 1 monitor on the HDMI port, 1 on a displayport to HDMI adapter, and one on an ACTIVE displayport to DVI adapter. I'm thinking that the trick here is to use an Active DVI adapter (mine is from Accell)