Apologies for the delayed reply
a) Magic sword held by undead enemy that among other things does Negative Energy "damage" to wielder
Mm, although there is a 'Drinker' weapon enchantment, it simply grants Hit Points to the wielder (not specifically positive or negative energy). Instead, I'd suggest a constitution penalty attached to the weapon. Or better yet, a vulnerability to cold energy damage (with the original undead wielder being immune to cold damage, so that the penalty wouldn't apply to him).
b) Specific companion item only that is not removable from item slot - for instance cloak for vampire that allows it to survive under sunlight and for immersion purposes just cannot be removed, or heirloom item
Yes, it will be good for companion heirlooms and such.
c) Class specific item, sword/potion only for thief to use. This as I understand is doable now with Coding/Changes field, so it is kind of moot now.
Indeed, it will be good for Rogues. Not yet doable but I'm planning to add that feature. (I want to have some Rogue-only items in The Dark Arena)
d) Item with great stats most of the time, but at times useless against certain foes cause they are immune to it, item is cursed so it cannot be immediately removed, which could be troublesome if your main damage dealer needs to switch for something else to cause damage. In short a tempting item with a twist, basically variation of item from b).
I guess it could be done, for example there could be a nice Greatmace, which deals bludgeoning damage, but the enemies have a high Damage Reduction bypassed only by slashing weapons (e.g. DR 20 / slashing).
e) Pure cursed item, sure reload solves this, but many people don't like reloading, or party is simply captured and given collars and have to follow orders and the collar is unremovable until certain point.
Yup, the collar thing sounds nice.
3) In mind I had stat nerf mostly, like for vampire -10 strength outdoors
Actually, maybe it can be done already without changes in game code. If the vampire is a companion, I'm guessing it could be done using a script that gives an ability reduction to that character as soon as you enter the outdoor map (you can use the script command used to give conditions to characters for that, please scroll down to the bottom of the list of conditions to find the 'ability reduction' choices). Then you have to make sure that the script used to leave the place removes that effect (or have the effect be day-duration only). In addition to the ability reduction, or in replacement of it, you can give the Slowed condition.
map wide constant low elemental damage in certain areas at regular intervals, ie freezing (it is there in some way already I noticed)
Yup, freezing, sweltering and underwater are already there in the game as possible map-wide settings.
"Dead magic" is an interesting suggestion for another map-wide setting, thank you.
Some extra settings that could be added include "Ozone" (electricity damage doubled), "Sulphur" (acid damage doubled and 1d4 acid damage when moving around), "Storm" (wind and lightning spells more effective and penalty on ranged attacks).
Also I would like to add 2 effects to a single healing item, normal d6 restore hitpoints + restore all spells slots, so far upon use it either does one or the another, but not both.
Mm, looks like it's a limitation of the engine for now. I would need an extra line saying specifically "restore d6 HPs AND restore spell slots".
I would like to know if it is possible by script or any other means to lower or permanently remove Spell Resistance from my party members, especially wizard?
Yes, it can be done using the script command that grants a condition to a character. Input "{ALL PARTY MEMBERS}" as the target. Select the "Lowered SR" condition and use the "amount" field to specify by how many points the SR should be reduced. That should work.
Have a great time! Best regards