If they are deformed, pulling them out early won't change a thing. Cutting early and handling eggs to often does more harm then good. Day 58 is not late by any means.
Honestly, in my opinion, you have more to loose then gain by disturbing them this way. True, sometimes you can intervene if they are in trouble, but even then, it usually doesn't end well. And far more often trouble is actually caused by cutting/handling/disturbing the egg/hatchling to much or to often.
I had one vertical egg in my last clutch. That hatchling didn't seem to have any problems at all because of the position of the egg. I think you risk more by changing the position, the hatchling could scare/spook and try to put himself back in his former position, getting all tangled up in the process or drowning.
I can't tell you what to do . Sometimes its a "damned if you do, damned if you don't" kind of situation. You will have to make the ultimate choice. But what I can say is that in my many years of reading/learning about Ball Pythons and owners experiences, taking one out of the egg early rarely ends well.
I wish you best of luck, it would really be a huge bummer if you lost this snake after working towards one like it for so long!!! I'm crossing fingers and toes that this little one is just chilling and taking his time, and will come out looking great when ready !!
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