A few things:
• OOTP injury frequency is based on a much larger sample of data than what you've looked at; it's based on a database of more than 1000 injuries. The last time I checked (which was last year if I remember correctly), the frequency of long pitcher injuries was slightly too low, and the frequency of long batter injuries was too high. That should still be true, since I don't think anything was changed, code-wise.
• I don't understand some of the distinctions you're drawing when you subdivide your data. You seem to be regarding 'torn UCL' and 'Tommy John surgery' as different injuries, when they're the same. OOTP often uses different names for the same injury, because that helps to make certain injuries more common, for reasons I could explain but the explanation would be boring.
• within the injury model in OOTP, it's extremely difficult to control precisely the frequency of individual injury types. That's just because of the injury architecture OOTP uses now; it's not designed to do that. Really the best we can hope for is to get the right distribution of short and long injuries, and the right distribution by body part. But when the game wants to give someone a leg injury, it's basically impossible to make sure it picks 'strained hamstring' the exactly correct percentage of the time.
•*OOTP doesn't distinguish among types of arm injury now. A shoulder injury has the same effects as an elbow injury. So if you're finding that the proportion of shoulder injuries is too high relative to the proportion of elbow injuries, that's only a cosmetic difference. It doesn't have any effect on game results. I'd like OOTP to properly account for the differing effects of shoulder and elbow injuries, though we'd need a bit more data on how those types of injury affect player skill (numerical data, not just the anecdotal observation that 'shoulder injuries lower velocity, elbow injuries hurt control'). OOTP does, however, use real life data to determine how, and how often, a pitcher's ability will be negatively affected by a serious arm injury; it just groups elbow and shoulder injuries together.