Hi SteveK,
I looked at your example song and it seems to me that you're using a Logic Multi to send MIDI to a Kontakt instance (in several cases). For example, your EW Brass 4 is cabled (remotely) to your EWBrass4 Audio Instrument Strip where Kontakt is loaded.
The problem with this kind of method is that you are severely restricted in the Arrange Window as well as with sending controller data, as you have discovered.
There is another way to achieve what you want. It takes a while to set up, but it's well worth it. Here goes....
THE CLONE METHOD:
1. Select your Audio Instrument in the Environment Window - eg EW Brass 4 (the channel strip with Kontakt loaded)
2. Name the strip EW Brass 4 Ch1
3. Set its MIDI Channel to Ch1
4. Option-drag the strip to make a copy (you may need to clear some space for this) - place it next to the original.
5. You have just made a CLONE of the first strip. You have *not* loaded a separate instance of Kontakt.
6. Set its MIDI Channel to Ch2 - name the strip EW Brass 4 Ch2
7. Keep making clones until you have 8 or 16 or however many channels you need.
8. Remember to set each new clone to the next MIDI channel and rename each strip.
9. You now have 16 clones of one Kontakt instance.
Now, instead of your old method of using channels of the Multi to control your score in the arrange window, use these clones.
Each clone will control a separate MIDI channel in Kontakt, but you'll find you can send all controller data that you need, specific to each MIDI channel. You can even use Logic's Automation and separately automate each arrange track where a clone is loaded - ie, you can automate parameters for each part within Kontakt. Going even further, you should find that when you enable Automation, that a unique menu for automating Kontakt parameters will pop up. (I don't have Kontakt but I use this method with Stylus RMX).
The one apparent drawback is that if you move the volume or pan controls of one strip, all clones are affected. The way past this is to use the volume and pan controls inside Kontakt, which you should be able to automate as explained above. eg Volume or Pan or Part 1 or whatever
Hope this makes sense.....
Regards - Colin