I hate to say this, but it's starting to sound like Glenn's Tennessee experience.
This is why I think it makes sense to go to a shop which specializes in Commanders, or at least which does a lot of work on them. They screw stuff up too, but less on the simple, stupid stuff. It may cost a bit more (or it may not), but it saves a lot of time and frustration.
When Aero Air did my panel, they were a few weeks late and there was some stuff which required some tweaking-- but nothing like this. Of course, they've done many, many Commander panels, and they really understand where the pitfalls are.
They did my Citabria ADS-B and GTN installation, and I was a bit nervous about that, since I don't think they knew what a Citabria was before they started. Turned out fine, though, with really no issues, but then that's a very simple installation.