Reading through this thread again (sorry I disappeared after posting my original question), I think I've misunderstood the question.
The way I understood it was "I want to program my synth to change over time" but I think it's really "I want to program something in, loop that, and then send extra notes/controls/whatever while it's looping, without recording those"
If I've understood correctly, the solution is to make your clip with whatever you want in it, and trigger it so it starts looping. Make sure your MIDI track has the appropriate controller and MIDI channel as its input. Set monitoring to AUTO, and arm the track for recording. so both the data in the clip and the MIDI from the controller are recognized. Turn off the OVR switch at the top of the screen, so nothing gets overwritten or recorded. You don't have to hit the global record button at the top unless you want to record what you're doing in Arrangement view.
I'm doing this from memory, but I think the basic idea is there. Someone correct me if I messed up the specifics.
Anyway, this works fine for notes and pitchbend/modwheel. I think it works for other CCs too. For modulating things like filters though, I prefer to use Live's parameter mappings, so I enable "Remote" for my MIDI device in MIDI preferences and then use the everything-goes-purple MIDI mapping to assign some CCs to those parameters. If I'm using a VST, I'll use the Configure button on the VST device to get some Live-mappable controls to show up.
Hopefully this was of some help to you? Sorry it's been so frustrating, it sounds like you've been approaching the problem well though (checking manuals, support, asking questions, etc).
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