I know that these are small businesses. I know they have families to feed. I don't feel like being the jerky customer who escalates complaints. But I also feel like there's no reason for a customer to be treated this way. Am I doing something wrong here? I'm just feeling very frustrated.
Your feeling of frustration is both understandable, and probably justified. I use the term 'probably' simply because we have one side of the story - yours. But, there is certainly no reason to doubt it.

I cannot think of anything you are doing 'wrong', based on your description.
The perceived competence of a dive shop is based on their attentiveness to customer needs. Yes, having a knowledgeable staff, a good selection of merchandise, and reasonable pricing are all part of that attentiveness. But, paying attention to, and serving, you as the customer is what makes a 'good' shop. And, yes, they are 'retail' operations and selling things, be it gear, training or travel - for a PROFIT - is what they are in business to do. There is nothing at all wrong with that. It is a good thing. Unfortunately, some shops seem to forget that the customer is doing them a favor by shopping there, not the other way around. (One of my sons-in-law is a partner in a restaurant. The senior partner has a business philosophy that I can really relate to - 'My job is to relieve you of as much of your money as I can, and have you feel good about it.')
Three thoughts come to me based on your shop descriptions:
1. It is interesting that you elected to not to go with shop D, after what you 'had a great experience and feel I got a very good training with them' for open water. It might have been more productive to speak with the shop management about your less than positive experience in the specialty class - let them know your concerns, and ask them if that is their norm. That way they get to know you better, understand that you are serious about the quality of training, etc. Plus, it helps them understand that large classes might not be everyone's preference.
2. The problem with shop X appears to be that they are one of the shops that take 'personal' offence when a customer chooses to go elsewhere. Instead of trying to better understand WHY the customer went elsewhere, they simply want to piss and moan that the customer did so. Unfortunately, there are shops like that out there. Fortunately, they are a minority. And, you learned a valuable lesson - don't use them again, for anything.
3. With regard to getting your cards from shop J, I suggest that you call them, and find out if they physically have the cards in the shop - they may need to look a little harder. If they do not, find out why - were the cards mailed to the shop by SDI and the shop then mailed them to you? (Or, were they supposed to be mailed directly to you by SDI?) If they were mailed to you by the shop, and for some reason a wrong address was used, they should have been returned to the shop. If they do have them / are able to find them, drive the 180 minutes to that shop and back and pick them up. While you are there, speak with the owner, and let that person know that you are very disappointed with your experience. It is always better to handle things like that bin person, instead of being a disembodied voice on the other end of a phone call.
My own experience has been that, if you invest in the relationship you have a better chance of reaping benefits. Spending money is an investment. But, becoming a person known (positively) to the shop staff is equally important.
To address the title of your thread: There are many good shops, and I do not believe the majority are bad by any means. I 'grew up' in one of good ones. I started diving when I completed my OW there, and I ultimately progressed to Instructor through that shop. The owner and I became friends, travel companions, dive buddies. The shop had a base of customers who were loyal to the shop - many of them would stop by from time to time just to chat, whether they needed to buy anything or not. As a member of the instructional staff, I felt like I had a home away from home. Unfortunately, the shop closed ~5 years ago after the owner died suddenly at a young age. To this day, the Instructors who were part of that shop like to refer to it as Camelot.