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Ok a few things to note here.

In the xui xml append you don't need the ruleset appended to it. And you will want the open backpack and close compass bits as well. So it should be like below.

<xui>

	<append xpath="/xui/ruleset" >

	<window_group name="workstation_scholarDeskFap" controller="XUiC_WorkstationWindowGroup" open_backpack_on_open="true" close_compass_on_open="true">
		<window name="windowCraftingList"/>
		<window name="craftingInfoPanel"/>
		<window name="windowCraftingQueue"/>
		<window name="windowToolsScholarDeskFap" />
		<window name="windowOutput" />
		<window name="windowNonPagingHeader" />
	</window_group>

    </append>
</xui>

In the blocks xml you will want to set a crafting area recipes. So something like below.

<blocks>

<append xpath="/blocks">

<block name="scholarDeskFap">
	<property name="Class" value="Workstation"/>
	<property class="Workstation">
		<property name="Modules" value="tools,output"/>
		<property name="CraftingAreaRecipes" value="player,workbench"/>
	</property>
	<property name="CreativeMode" value="Player"/>
	<property name="DescriptionKey" value="scholarDeskFaphDesc"/>
	<property name="DisplayType" value="blockMulti"/>
	<property name="WorkstationIcon" value="ui_game_symbol_workbench"/>
	<property name="WorkstationJournalTip" value="scholarDeskFapTip"/>
	<property name="Stacknumber" value="1"/>
	<property name="Material" value="Mmetal"/>
	<property name="Shape" value="ModelEntity"/>
	<property name="Model" value="@:Entities/LootContainers/deskMetalFullPrefab.prefab"/>
	<property name="Path" value="solid"/>
	<property name="ModelOffset" value="0,.5,0"/>
	<property name="MultiBlockDim" value="2,2,1"/>
	<property name="ImposterDontBlock" value="true"/>
	<property name="WaterFlow" value="permitted"/>
	<property name="CustomIcon" value="scholarDeskFap"/>
	<property name="Place" value="TowardsPlacerInverted"/>
	<property name="OnlySimpleRotations" value="true"/>
	<property name="IsTerrainDecoration" value="true"/>
	<property name="StabilitySupport" value="false"/>
	<property name="Weight" value="0"/>
	<property name="EconomicValue" value="1000"/>
	<property name="TraderStageTemplate" value="midTier1"/>
	<property name="MaxDamage" value="800"/>
	<property name="HeatMapStrength" value="0.5"/>
	<property name="HeatMapTime" value="1200"/>
	<property name="HeatMapFrequency" value="25"/>
	<property name="OpenSound" value="open_workbench"/>
	<property name="CloseSound" value="close_workbench"/>
	<property name="TakeDelay" value="5"/>
	<property class="RepairItems">
		<property name="resourceForgedIron" value="25"/>
		<property name="resourceMechanicalParts" value="20"/>
		<property name="resourceDuctTape" value="25"/>
	</property>
	<drop event="Harvest" name="resourceForgedIron" count="5" tag="allHarvest"/>
	<drop event="Harvest" name="resourceForgedIron" count="5" tag="salvageHarvest"/>
	<drop event="Harvest" name="resourceMechanicalParts" count="8" tag="salvageHarvest"/>
	<drop event="Destroy" count="0"/>
	<drop event="Fall" name="terrDestroyedWoodDebris" count="1" prob="0.75" stick_chance="1"/>
	<property name="SortOrder1" value="B281"/>
	<property name="SortOrder2" value="0300"/>
	<property name="Group" value="Basics,Science"/>
	<property name="FilterTags" value="MC_playerBlocks,SC_decor"/>
</block>

</append>

</blocks>

The above uses two crafting area recipe lists as an example. This can be changed to whatever you like and be just one list if wanted as well. To have recipes use a custom craft area recipes list you will also need to make recipes that use the same craft area tag. Just checkout some of the vanilla recipes in the recipes xml for the vanilla workstations and how they use the craft area tag.

The grid in your tool window in the windows xml doesn't need repeat content set to true if using only 1 tool, also might double check tool spelling as well, any typo can throw everything off. So should be something like below.

<windows>

	<append xpath="/windows">

	<window name="windowToolsScholarDeskFap" width="228" height="121" panel="Right" cursor_area="true">
		<panel style="header.panel">
			<sprite style="header.icon" sprite="ui_game_symbol_pen"/>
			<label style="header.name" text="TOOLS" text_key="xuiTools"/>
		</panel>
		<rect name="content" depth="0" pos="0,-46" height="75" disablefallthrough="true" on_press="true">
			<grid name="inventory" rows="1" cols="1" pos="3,-3" cell_width="75" cell_height="75" controller="WorkstationToolGrid" repeat_content="false" allow_sort_order="false" required_tools="scholarPenFap" required_tools_only="true">
				<required_item_stack name="0"/>
			</grid>
		</rect>
	</window>

	</append>

</windows>

And then lastly you may need to make an entry for your workstation in the ui_display xml, check the vanilla xml and look for the crafting stations towards the bottom of the file for examples.

Hopefully this helps, come on back and let us know.