I didn't see the first draft, so this is all fresh..."Calvin didn’t like this bar, he didn’t like it at all."
I believe that you need either a period of semi-colon between he and bar. I would go with a period. I think it puts the emphasis in the right place.
Otherwise, good opening sentence. It already creates tension. What's he doing ina bar he doesn't like? Why doesn't he like it? Good questions to have going through my mind.
" It was dark, stuffy, smelly, and scummy, mostly scummy."
If you keep this sentence, I think that you need a '--' between scummy and mostly scummy. But I'm not sure if this is a good follow-up to what you had before. For one thing, it doesn't give me any new information. For another thing, this is a good example of "telling" -- I'm sure you've heard "show don't tell." Well, here you are, telling me that a bar is dark, stuffy, smell, and scummy. If this is important, I'd rather see it more clearly.
" He would never tell Greg, the owner, though. Best friends didn’t dothat to each other. "
Interesting and not where I had expected this to go.
"He only sought sanctuary, he wouldn’t be here if he wasn’t. It wasn’t even an hour ago that his rivals and so-called protectionists had blown his restaurant apart. "
This is where you lost me but it shouldn't have been. This is the story problem. This is your hook. For one thing, I'm not sure what you mean by "so-called protectionists" and it's bugging me. For another, I think you could have said all this in a much, much shorter paragraph. I think it could have all been one sentence, without nearly as many was's. (I'm not the "to be" police or anything, but being creates a sense of standing still and this is a part of the story that I think you would much rather see moving.)
"His hand shook as he saw blood from a bullet wound seep through layer upon layer of cloth."
Doesn't he feel the bullet, too? I would like more detail about this from his point of view. Try to add sensory details -- not just sight but smell, taste, sound, and texture.
" Next to him on the counter was his clarinet, his prized possession and only connection he had to his past."
Suggestions: reword to remove the was. Otherwise, another good detail. I expect the clarinet to be important in this story.
" Next to that sat a half-empty glass of scotch; he wasn’t a drinker but this was not normal circumstances."
Should either read "this was not a normal circumstance" or "these were not normal circumstances." (verb-subject confusion) I also think a period would work better than the semi-colon here, but that's just because I like the stacato of short sentences driving forward tension.
" The low light in the bar cast a reflection on the polished surface of the counter."
I don't expect to see polished counters in a scummy bar.
" The face looking back at him was pale and drained"
For one thing, physical description through reflection is something best used sparingly. For another, it feels entirely forced in this situation. Especially since I wouldn't expect a polished counter and because I can already imagine that his face is pale and drained. You've already convinced me that he's not well so I would say move on.