TR_m4_q_Ancestral_AmuletScrpt

startscript TR_m4_q_TTSJournal

starts a global script targeted by default on the object that's been activated, and since that object is set for deletion afterwards that's trouble. there's a bug when later reloading a save, that global script would become targeted on the last created object and make the vanilla engine crash if said object is activated... just need to give the startscript an explicit target, player->startscript TR_m4_q_TTSJournal
also it's not important but the DoOnce variable serves no purpose in this script after the check is already done by GetDisabled

TR_m4_q_Ancestral_Gh_scrpt

 note that OnDeath is a one frame only event already (the extra DeathCheck isn't necessary in this script)

if ( GetJournalIndex "TR_m4_wil_TribunalTS" >= 98 )            ;the ghost just goes away if you complete the quest
    disable                                                                    ;no getdisabled check as it already is there above whene enabling it
endif

don't know if I understand the comment correctly but the beginning of the script enables when GetJournalIndex "TR_m4_wil_TribunalTS" is 30 or more, so this would be disabling again every frame, should just move it to the beginning too?

TR_m4_q_Corane_Morianne_scrpt
 

    elseif ( GetJournalIndex "TR_m4_wil_TribunalTS" >= 30 )
        Set State to 0
        Set State2 to 1
    endif

    Set State to 5

the State variable here will always become 5 after being set to 0, I haven't followed up to the dialogue logic yet but this must be unintended
 

         if ( GetJournalIndex "TR_m4_wil_TribunalTS" == 20 )
            if ( GetDistance "TR_m4_q_TTSAncestral_ScrptAmule" < 550 )
            if ( GetPos Z < - 175 )
                  AItravel -257.000 618.000 -256.000

you probably want to add the extra AItravel "reset" argument 0 or 1 (same effect AFAIK) like this
AItravel -257.000 618.000 -256.000 1
without that argument one effect is that if the player rests while the NPC is undergoing travel the next check for GetAIPackageDone won't be detected in vanilla.
 

if ( GetJournalIndex "TR_m4_wil_TribunalTS" == 10 )             ;Keeps track of days passed when you accept the quest but don't go in.
    if ( currentDay != Day )
        set currentDay to Day
        set LocalDaysPassed to LocalDaysPassed + 1

I remember this from vanilla scripts, unfortunately it doesn't work since it can only increase by 1 at a time, even if you've been gone for 7 days it will only count 1 day passed when you enter again

forcegreeting

just a general note that if you don't want the rest of the script to still run before dialogue has happened it needs "return" somewhere after forcegreeting

if ( TR_m4_q_FranDead )                                                        ;If Francessa dies, Corane will attack you
    if ( TR_m4_q_CombatState == 0 )
        SetFight 100
        StartCombat Player
    endif
endif

are both lines supposed to be called constantly, in this script and in TR_m4_q_Fran_Morianne_scrpt? not sure if there are any risks with using StartCombat every frame
 

TR_m4_q_Gilmaso_Olthan_scrpt

                if ( GetLOS player == 1 )
                    if ( DoOnce == 0 )

using this function every frame with no delays might cause slowdowns in the vanilla engine? DoOnce is checked an extra time above these lines

if ( DayTarget == 0 )
    set DayTarget to ( DaysPassed + 1 )
    set HourTarget to ( GameHour )
    return
endif

sets the next day as target the first time this NPC is ever loaded, even when no quest has started because when the NPC is disabled for the first time that part of the script will still run.
that's probably not intended? maybe you need to return after the lines that disable at the beginning of the script, instead of only when it's already disabled

TR_m4_q_TTSJournal
 

set ObjectCount to ( TR_m4_q_Corane_Morianne->GetItemCount "TR_m4_q_TTSAncestral_Amulet" )

...
                    if ( ObjectCount )

FYI you're allowed to check targets inside conditions like this
if ( TR_m4_q_Corane_Morianne->GetItemCount "TR_m4_q_TTSAncestral_Amulet" )

though if you needed something more complex like checking different targets on the left and right sides of a == or > sign then you probably would need these intermediary local variables

dialogue results

PlaceAtMe TR_m4_q_TTSBoneWalker 2 512 0
;PlaySound3D "conjuration cast"
TR_m4_q_TTSBoneWalker->StartCombat TR_m4_q_Corane_Morianne

TR_m4_q_TTSAncestral_Gh ->PlaceAtMe TR_m4_q_TTSBoneWalker 2 64 0
;TR_m4_q_TTSAncestral_Gh ->PlaySound3D "conjuration cast"
TR_m4_q_TTSBoneWalker->StartCombat TR_m4_q_Corane_Morianne

may not work as intended, at best the first or last one of the TR_m4_q_TTSBoneWalker that are created should get targeted by that command to attack the NPC (and since the bonewalkers don't exist yet if even one does get targeted at all it would only be because this is in a dialogue result, compiled scripts wouldn't be able to) - the bonewalkers would need a local script on themselves for both to attack the NPC

TR_m4_q_TTSAncestral_Gh ->PlaceAtMe TR_m4_q_TTSBoneWalker 2 64 0

there should never be spaces just before or after "->", in some cases it consistently fails (maybe not here, I think it's IDs with spaces in quotes)

TR_m4_q_CombatState
when changed scripts will need to be recompiled - it isn't distinctive enough for a global variable, just missing something about the quest in the ID to make sure it's unique
TR_m4_q_GhostDead
same, TR_m4_q_CoraneDead and TR_m4_q_FranDead at least have less generic names but ideally all globals should be marked with something more like the quest initials "TTS" that the scripts have

general comment: it's much easier to use the tab key to indent than multiple spaces