Hey Burr,
Okay, I was able to get Mainstage 1 and Guitar Rig 3 talking okay. I'll outline here how I got the two to talk but I probably need a bit more info to address your exact need(s). I've also re-read your posts and I'll take a stab at what I think you might need to do to get set up a little better. The caveat here is that I'm not 100% clear on what you want to do, so apologies if I make assumptions that are a little off 😉
Since it sounds like you want to do MIDI patches and Guitar Rig patches and you're trying to separate the two, then let's look at that, we can always look at combined patches later.
So what it kinda sounds like, is that you're thinking about Guitar Rig at the concert level, the best thing is for you to think about Guitar Rig at the patch level. What that allows you to do is to create two different sets within the concert, one for your MIDI patches, and the other for Guitar Rig patches.
That way, you can navigate to whatever you want (MIDI patch or Guitar Rig patch) and not worry about the MIDI channel separation issue. When you were saying the Yamaha MFC10 was sending program changes for patches at the top level, instead, what you want to think about is using CC's (not PC's) for set and patch navigation and PC's only for direct access to a specific patch.
So, first program your MFC10 to send 4 different CC's for Mainstage navigation (Set Up, Set Down, Patch Up, Patch Down) e.g. you could use switches 7,8,9,0. Then go into Mainstage at the layout level and map the Set Up, Down and Patch Up, Down icon/switches using the MIDI Learn function. Go into Edit mode and test the navigation.
Next, create two different sets MIDI and Guitar Rig.
Then create your MIDI patches in the MIDI set as you normally would.
Create your Guitar Rig patches within the Guitar Rig set. Create separate Guitar Rig patches using the MFX stereo version of the AU plug in for GR. When the Guitar Rig plug-in window opens, select/edit the patch within Guitar Rig that you want to use. That specific Guitar Rig patch will now be saved in your Mainstage patch. Set up a separate Mainstage patch using a Guitar Rig patch for each of your different patches/songs.
Now you can go into perform/full screen mode to navigate to each set or patch using switches 7,8,9,0 (if that's what you used) of your MFC10 and that will call up you patch.
Additionally, if you want to call up a specific patch from MFC10, then program one of your MFC10 switches to send a specific Program Change. Then click on the patch in Mainstage, the Patch Inspector window will open up - now assign that same Program Change number there. Your MFC10 will now call up that specific patch when you press on the switch.
Now, the next thing is...if you then want to modify or express something WITHIN a Guitar Rig patch. Then you first have to program your MFC10 to set up/send let's say...5 different CC's so let's use 1-5 of your MFC10. We might want to turn on/off different effects for example, or boost a gain, or whatever. In this example, we'll choose turning an effect on/off.
So program your MFC10, then go into layout mode in Mainstage and assign the stompbox on/off switch by clicking on it, using MIDI Learn, and then pressing your footswitch to learn the CC.
Go into Edit mode, select your Mainstage Guitar Rig patch, then click the stomp button(s) you just programmed. The parameter mapping section then opens up at the bottom. Choose your Mainstage patch name (appears right under "Parameter Mapping".
Then the next column (to the right) populates, choose "Guitar Rig 3 MFX", the next column then populates with all the Guitar Rig 3 parameters, select whichever GR3 item you want to control and do the parameter mapping. In my test I chose Skreemer On/Off because I mapped my FCB1010 and Mainstage Stompbox to switch that effect.
Anyway, if everything was done ok then when you press switch 1 on your MFC10 it will turn the effect in Guitar Rig 3 on and off through Mainstage.
So now knowing all that, you should be able to map Mainstage and GR to do what you want by just using the same principles.
Sorry for the long explanation but it's the only way to give you the details...I hope I got what you wanted to do after all that...phew 🙂
Give it a go and let me know if you have any questions.
J.