For now, I spent another day nailing all the missions md, and double checking errors in debuglog...no error now. Remains to be seen if the changes I added work but they were not dramatic, mostly I helped the vanilla missions to work (also I had already moved some sectors in previous sessions), so here it is, the candidate to be final

XRSGE 2.8
https://www.nexusmods.com/x4foundations/mods/507
...no significant issue remains on the radar (if this last version works as intended). For as much I could check, all sHWs work perfectly now but any small correction won't require a new game.
Just to be sure, if continuing an oldcsave, open console and type "/REFRESHMD" exactly as I wrote it, without brackets. Game should freeze for few secs. This willl update missions. Only needed for old saves oc
I still have not tested the new patrols either, but they'd be significantly reduced and are another thing that can be changed later without breaking the game. Stories had top priority

Please if you report issue, always specify if it is a new game start in 2.8 or not