Unfortunately I doubt anyone knows this software and/or can assist. I'm using PCAD 2006 and the components are designed around layers designed from my old company.
I shouldn't have made this statement. First off, EEVblog has been amazing with helping with answering questions. Secondly, this site is comprised of people who have decades of experience.
Minutes after I sent that message, someone sent a private message who knows PCAD and helped me.
The libraries I have for PCAD have unique layers, so my mindset was that I can't be helped due to (technically) being unable to share any of the libraries since they were at one time designed for my old job (even though they are just basic components).
So I felt that if I can't share the libraries, I certainly can't ask for anyone to guess at trying to solve issues.
Having said all this, it appears I finally got a successful acceptance of my design and it's being fabricated.
I asked these questions to the person who sent a private message, but I'll ask here too for others to benefit (I'm still waiting for a reply from the person, but know I'll get a response).
Attached is the options for N/C Drill. My design was done in mm. If I select 'inches' (which seems to have been the selection accepted by JLCPCB), will that cause conflicting information between gerbers and drills?
Also, the rest of the options I don't know what they mean. In the past I may have left them as is and never had an issue, but now I did and don't know what these mean. So if I have issues in the future, I won't know why they need to be changed.
Last question is: if these settings were wrong, why was it reported that I was "missing" drill files? Did their software just overlook the file because it wasn't formatted properly?