You said that the dabase structure is the same, as you can see on attached file the two structure are different..
V4 has two tables more
Anyway, i've fixed my live install with JM 3.3.1 and Joomdoc 4.0.2, to solve permission problem i've open and salve all my documents one at a time and set the right permission because global does'nt work

If you need to do some test about v3 to v4 migration i can send you a backup of my previous site based on JM 2.5 and JoomDoc 3.4

let me see..

Hello, I do not know. Permissions is question of Joomla core. Nobody has such problems as you. Maybe try to do completely fresh installation to fix it.

Sure, your software is perfect and i'm only one with problems...
look:
extensions.joomla.org/extensions/directo...tion/downloads/8620/