I will say I was frustrated going from 9.5.3 to 10.0.1, even after testing, reading, and using before I moved my clients over. I did not do a straight upgrade on the same machine because through reading and testing I discovered the vast differences between the two versions. I wanted to add the billing system because my previous provider would not allow or support it, so I set up 10.0.1 on a brand new server while my current clients stayed on the old 9.5.3 server. I slowly added clients to the new panel/business manager before moving their data over. I didn't have the luxury of using the migration tool as my provider did not actually give full root access. The new 10.0.1 server is with a new cloud based provider where I have complete root access.
I made and downloaded backup files of each domain and transferred them to the new panel in small groups. I later found that the pre10-backup-convert script was not documented very well, which was the main source of my frustration. 2nd-line support was able to help me by coming up with specific routines to correctly convert and restore domain settings, content and databases for each client. I believe they will be posting a KB article soon which detailes the process. It wasn't easy or a walk in the park, but it is stable now and I have a fully converted client base using Business Manager on the new server. In the end, I think it will be worth all the trouble.