ok, because it just won't leave my mind, here is a list of everything crystal related since the space hulk incident. to see just how much pull crystals had an effect on the quest and to see if feasible to salvage if needed
THE LIST
Turn 7: Space Hulk
obtained
-concept crystals: Order, Fire/heat, Ice/cold, Electricity, and Darkness crystals
-gummi block things
-distracted chaos
-malal's return
Turn 8
-talismans for psykers and army people
-booster crystals
Turn 9
-Gellar/blank crystals (bonus to ship perils of warp rolls)
-talismans for weapons
-anti warp corruption artifacts around children centers
-runic research (not sure this counts as it is said in description that the idea of concept crystals inspired serras and plus they existed already with the space wolves AND Serras knew about rituals so possibly could have thought about miniaturized rituals in way of runes)
Turn 10
-created crystals/runes and talismans for: Speed, Penetration, Preservation, Defense, Protection, Healing, Earth, Water, Air, Magnetism, Gravity, Metal, Light, Sound, Space and Time.
-improved talismans
-Guidance, Purity, Accuracy, Detection, Organization and Balance crystals/runes made (bonus to pdf rolls)
Turn 11
-communication and navigation crystal and rune made
-FTL communication (no real effect seen yet)
-Eldar trade deal, lose three point on our side, most likely need to give up on wraithbone in beginning till we make soul stones to trade for it or ask the elder gods for it, chance of reroll needed due to point difference (still gain elder advisor SL, and elder alliance, actually not sure this goes here since we can get alliance anyways even without offering any crystals as long as we do not ask for advisor or wraithbone)
Turn 12
-souls storing crystal/soul stone (?)
-Wisdom, Time, Concealment, Self and Purity and Will Power crystals/runes, bonus to anti chaos/cults/demons
-willpower gauges (replace talismans with equipment with etched runes?)
-self rune
-psy gear with wraithbone (?) (possibly made later or at same time we did it now if we focused more actions on soul stone and asked to trade it for wraithbone and/or advisor)
-begin orichalcix (not sure this counts again as wraithbone possible gained without crystals)
Turn 13
-crystals to Magnus and his brother
-talismans for navigators, does not affect better nav equipment (also done on either turn 12 or 11)
-improve Gellar fields with integrated crystals and runes (can just remove crystals, lower bonus, and keep as normal)
-improved willpower gauges (replace talismans with equipment with etched runes?)
-talismans for psyker training tools
-gained webway acess (?)
-arcology design (just need to edit numbers due to reduced effectiveness from no crystals? or keep same by developing needed runes instead)
-crystals sent to Emperor, thunder warriors stabilizing(?) (saved thunder warriors?)
Turn 14
-Crystals to Dorn and Leman
-crystals used to protect stellar bellows against chaos (will need new way to protect it, likely a lot of runes and possibly soul bounded, runed kill switched psykers)
-webway clearing (likely reduced clearing speed due to removal of concealment crystals and other crystals)
-advancing/maxing crystals
-birth of crystal god (replace with Rune God? I mean rune PRIESTS are a thing so....lol Russ replaces Lorgar as religious primarch, or maybe they bond hmmm)
Turn 15
-replace all crystals in minor plan with runes to develop rune god
-replace booster crystal with booster runes? (meditate with rune on body to enhance stat via absorbing knowledge from the warp?)
overall change: reduce psyker checks due to no more crystals, perhaps keep if given bonus to the runes instead? hmmm.
not sure if I should even count the runes in this list as they can still be made just with a higher difficulty
OVERALL SITUATION: Not as bas as I thought, would take a bit of time, but is possible to replace all mentions of crystals with runes instead if needed. Along with removing Malal and any mention of KH, though possible to keep Malal and just say he finally developed Malal daemons to fight in the warp for him besides empowered mortal servants
I'm tired.
edit: forgot when chaos tossed orks at us, but not really important