You can leave Maxos temple and finish off the remaining areas of Broken Valley, then return to confront Amdusias.
The crystal skull is in a mine to the far west of Lovis' tower, to the south of the fortune teller (there was / will be a cutscene as you enter the camp, with a dying miner telling you about attacks in the mine). The necromancer has basic body parts you can use for your creature, but they don't have bonuses as good as the ones you can find (or later buy from a specific merchant).
Plant material can be used to make potions, as long as you have the formula. Check out the cellar of the miller's house in the village...
The key for the hatch is in a pot in the kitchen; move some lettuce, or something, and a few potatoes to find it. You can mindread the miller to get a clue where it is, but do not need to (or didn't in D2:ED).
Minerals and gems can be used for enchantments, also requiring a formula. The enchanter is to the far west of Lovis' tower and then north. Unenchanting an item will give you the formula, if you don't already have it.
If you talk to the necromancer, alchemist and enchanter in Broken Valley, and go into the appropriate create creature / potion / enchant functions, any body parts or formula will be added to their selection. After that, any left in your inventory are duplicates, and can be sold.
After you complete Maxos temple, you will get access to Sentinel Island. Your first encounter there you can mindread to go up a level, so the higher level you are (In D2:ED I made it to level 18 in the fjords) the more of an experience bonus that will be. You don't need to get to a high level, but it would be better if you got to a new level before entering, to get a full level bonus.
