We ran the Parallel migration tool and converted the data for three of the companies we migrated.  Should I convert all companies before continuing testing even though I may not test in all companies?

Did the custom panels exist in the three companies you copied? 

Search the MAS90 folder for "M4L" files... the customized versions should be in MAS90\##\Custom\?-?\... (where ## = module code and ?-? is the scope...).  The migration tool should copy "All-All" panels, and panels for the selected company codes.

Did the custom panels exist in the three companies you copied? 

Search the MAS90 folder for "M4L" files... the customized versions should be in MAS90\##\Custom\?-?\... (where ## = module code and ?-? is the scope...).  The migration tool should copy "All-All" panels, and panels for the selected company codes.

Yes.

If you open those panels up in customizer, are the changes gone?

They are still there.

To make some custom panels reappear, I needed to adjust something on them and resave them.  Should I begin doing that as a standard practice on upgrades?

If you have something you can reproduce, report to Sage support for review.  That is not normal.  The update panel utility should be sufficient.

I had a similar situation and the only way I could get the customized panels to work properly in live company is to copy them over to test company and rebuild them and copy them back to live. For some reason rebuilding them in the live company did not do anything. This was an upgrade from v2017 to v2022.