Its just on par with learning new stuff, it happens. You tore down and built the machine, which is a feat. You're not a machinist by trade, but just being active on forums and reading helps a lot, which you do. Also, finding things to adjust, fix, or improve on a lathe will probably keep happening till they start throwing dirt on you, haha.
Kinda funny story from my younger days. More mechanic related, but I think it helps with machine work too. I spent a large part of my career, and early learning part, haha, with an outfit from the north east coast. The owner and the shop foreman were two really smart guys. Knew not only the business, but we're hands on types. They knew every inch of what we did, that they could troubleshoot blind all the time. That's the good, lol.
The bad is, they we're both harsh SOB's. Screaming and hollering all day. It was like working for 2 Sgt Gunny's from Full Metal Jacket. Harsh, but funny if it wasn't you, lol.
A line from the owner: "USE THESE THINGS !" Pointing at your eyeball, damn near touching it. "MAYBE YOU'LL SEE WHAT THE F#%* IS WRONG !"
Shop foreman on phone to road mechanic: "LOOK, TOUCH, FEEL. YOU'RE THERE, I'M NOT. YOU TELL ME WHAT IT'S DOING, WTF !"
Yea, it was a good time, lol. But taking those beatings, kinda drove people to think more. Run the process of what ever it is we we're looking at through our head. Not just thinking of the problem, but running the machines working process through our head.
Troubleshooting is a high percentage of what I do. I like to run a game of prove/dis-prove in my head. I want to be right. So I need to prove my self correct. But you can get short sighted, if only looking to be right, and overlook other things.
So whatever my working theory on a given problem, I try to prove it wrong. By working to both prove my theory right, and wrong, I start a chain of process of elimination. And as a side to that, I'm running the given machine's working process through my head. How it works, and why it works.