finally getting to it on my workstation.
--analyze’s output ends with:
One or more files are both in /usr/lib/ and /usr/lib64/, making the conversion impossible.
Please report a bug at https://bugs.gentoo.org/, and do not proceed with
the migration until a proper solution is found.
I think we need to figure out which packages own those files and report to the individual maintainers?
the tcl ones match puredata-base/pd, which no longer seems in portage or overlays.
in any case, those are installed both places by the same ebuild and should therefore not prevent merge.
the first three are more interesting.
one is sci-libs/med vs sci-libs/libmed, where the latter seems to be an old name of the former.
the mozilla one is installed both places by app-admin/lastpass-binary-component.
Dead packages obviously won't be fixed. If you could uninstall these that no longer exist and try again, that'd be great.
Please test removing the old software. The situation seems to be a bit more complicate and requires some analysis.
We can not help you efficiently via bug tracker. The bug tracker aims rather on specific problems in .ebuilds in the tree.
I have had very good experience on the gentoo IRC  with questions like this. Of course there are also forums and mailing lists [2,3].
I hope you understand, that I will close the bug here therefore and wish you good luck on one of the mentioned channels .
Please reopen the ticket in order to provide an indication for an specific error in an ebuild or any gentoo related product.