Does anyone have any experience with or knowledge of anyone who has filed an Article 138 UCMJ?

My recommendation would be to see the IG. Couple reasons I say that is:
1. While the UCMJ and manual for courts martial feels like an easy read; it isn't. Preface your concerns with "I believe" the Commander is doing x and think it's under 138. Here's the documentation that backs my belief. Let the IG figure out what article supports or doesn't support your perception.
2. The IG pathway gives you some cover from overt retribution if you're incorrect in your perception. I was always a chain of command guy, but in instances of perceived wrongdoing and potential UCMJ action against a field grade officer or higher in a command position is a sensitive issue and you need your ducks in a row. As a CSM if a Soldier brought an accusation against a Commander to me that would be my first phone call.

It's good that you are asking the question here before moving forward. There are many outstanding SGMs and others who can offer great advice and mentoring for you. Please do your research and listen to the Senior NCOs on this. I would recommend 1. trying your chain of command and if necessary seek approval to jump chain to any point where you feel you can trust. 2. seeking advice here and within your post from senior NCOs. 3. If 1 and 2 fail, contact your IG and be ready to defend yourself with documentation and credible testimony.

As Col Joseph Lenertz pointed out, documentation is key when going down this path. You will learn as you continue in the military that more weight is put on to have paperwork as you continue up the ranks and after. As a NCO, I carried a Leadersbook, as most do. I had everything within that folder not just for me but for my troops. It made getting things done from discipline to awards so much easier. Rather than scrambling to come up with bullets for their awards, I had it and thankfully due to the mentorship of senior NCOs who showed me how powerful a good Leadersbook could be I have carried that into civilian life. Today, I maintain a "LifeBook". Inside I keep things like my current lease, to my dog's paper work, children's report cards, military paperwork and other things that I find I'm asked for.

Whenever you are thinking of going down this road, you'll need that level of documentation because the last thing you want is to move forward without the proper background work which will result in setting yourself up for failure.