Ok here's the deal (IMO that is). I use roughly the same setup as you.
1. I really had to tweak patches I loved when recording direct to make them work in a live situation using the matrix and cabs. I primarily use the Diezel VH4 ch3 and the JCM 800 models. What I found for example is that marshall based models with the presence above 1.00 sound really harsh going through the matrix. So dial dowm the presence even if you wouldn't normally do it. It will sweeten your sound a lot.
2. I take it you use out 2 for matrix and cabs and out 1 for FOH right? Make sure you work with the sound guy using the global eq to get the FOH sound that works. Don't worry, that will not effect your Matrix/Cab sound which you can dial as you please. Of course your band having it's own soundman always helps.
3. Getting the levels right between cleans and dirty is something that requires a little time but you ll get used to it. You don't specify if you had a level problem level wise in the FOH sound or the stage sound. For the stage sound being a problem then I suggest solve it in the rehearsal room before the gig. now FOH level problem. As a place to start, and this is a mere pointer and not a must, try using the same cab configuration for all your patches. Levels differ greatly with different IR's and it's nice to have a stable starting point when you first attempt to tackle this issue.
4. Not sure if it's relevant but still worth mentioning, that when using the matrix, the sound disperses a bit differently than if you re used to using tube power amps. I feel like it's more "directional" in a way. Just keep it in mind and adjust your patches and/or cab position accordingly.
5. I trust you use your own cab right? Major issue. If not at least make sure you use the same type of speakers you made your patches on.
6. there's a video on the Matrix site on how to use the global eq to make the Matrix feel more tube like. Personally didn't do much for me but still give it a try.
7. there's a learning curve with the axe. I wouldn't accept it at first but there is. there's a learning curve in getting the direct recording sound you want and then just when you thought it was over, you change the application to a live environment and there's another learning curve. It's just the way it is. really. But IMO it is indeed worth it.
8. the tube guy you ll never get. I can guarantee that. There ll be always something missing from your sound according to the tube guy. trust your ears only.
hope I helped
Ravaya