With the help of Sarbian, I applied his diff from a binary KortexM had created

.gitattributes

@@ -0,0 +1,55 @@
+# ==================================================
+# Auto detect text files and perform LF
+# normalization.
+# ==================================================
+
+* text=auto
+
+# ==================================================
+# Plain text
+# ==================================================
+
+*.cfg       text    eol=lf
+*.CFG       text    eol=lf
+*.csproj    text    eol=lf
+*.CSPROJ    text    eol=lf
+*.md        text    eol=lf
+*.MD        text    eol=lf
+*.sln       text    eol=lf
+*.SLN       text    eol=lf
+*.txt       text    eol=lf
+*.TXT       text    eol=lf
+*.xml       text    eol=lf
+*.XML       text    eol=lf
+
+# ==================================================
+# Images & textures
+# ==================================================
+
+*.dds   binary
+*.DDS   binary
+*.png   binary
+*.PNG   binary
+
+# ==================================================
+# Binaries
+# ==================================================
+
+*.dll   binary
+*.DLL   binary
+
+# ==================================================
+# Source code
+# ==================================================
+
+*.cs    diff=csharp
+*.CS    diff=csharp
+
+# ==================================================
+# Ignore list
+# ==================================================
+
+.gitattributes export-ignore
+.gitignore     export-ignore
+*.md           export-ignore
+*.MD           export-ignore

.gitignore

@@ -1,2 +1,25 @@
+# ==================================================
+# Ignore selected folders and file types from the git
+# repository.
+# ==================================================
+
+Source/Builds/*
+
+*.db
+*.DB
+*.DS_Store
+*.ini
+*.INI
+*.lnk
+*.LNK
+*.pdb
+*.PDB
+*.png
+*.PNG
 *.sublime-workspace
 *.sublime-project
+*.user
+Source/.vs
+Source/bin
+Source/obj
+*.zip

GameData/ProceduralFairings/Config/PF_FilterExtensions_Config.cfg

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+//  ==================================================
+//  Add bulkhead profiles to all parts for FilterExtensions
+//  compatibility.
+//  ==================================================
+
+@PART[*]:HAS[@MODULE[ProceduralFairing*]]:FOR[ProceduralFairings]:NEEDS[FilterExtension]
+{
+	@bulkheadProfiles ^= :$:,proc:
+}
+
+@PART[KzThrustPlate]:FOR[ProceduralFairings]:NEEDS[FilterExtension]
+{
+	@bulkheadProfiles ^= :$:,proc:
+}

GameData/ProceduralFairings/Config/PF_Settings_Config.cfg

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+//  ==================================================
+//  Global procedural fairings settings.
+//  ==================================================
+
+PROCFAIRINGS_MINDIAMETER
+{
+    start = 1.0
+    miniaturization = 0.4
+    sandbox = 0.1
+}
+
+PROCFAIRINGS_MAXDIAMETER
+{
+    start = 1.50
+    specializedConstruction = 2.75
+    advAerodynamics = 4.0
+    heavyAerodynamics = 12.0
+    experimentalAerodynamics = 30.0
+    sandbox = 50.0
+}
+
+PROCROCKET_MINDIAMETER
+{
+    start = 1.0
+    miniaturization = 0.4
+    sandbox = 0.1
+}
+
+PROCROCKET_MAXDIAMETER
+{
+    start = 1.5
+    advConstruction = 4.0
+    metaMaterials = 12.0
+    aerospaceTech = 30.0
+    sandbox = 50.0
+}
+
+//  ==================================================
+//  Dummy parts to represent Procedural Fairings
+//  upgrades in the tech tree.
+//  ==================================================
+
+PART
+{
+    name = pf_tech_fairing04m
+    module = Part
+    author = Starstrider42 (config), e-dog (model)
+
+    MODEL
+    {
+        model = ProceduralFairings/Parts/base_standard
+    }
+
+    TechRequired = miniaturization
+    entryCost = 0
+    cost = 0
+    category = none
+    title = Procedural Fairings Upgrade
+    manufacturer = Keramzit Engineering
+    description = Allows fairings and plates to be made as small as 0.4 meters.
+}
+
+PART
+{
+    name = pf_tech_fairing2_75m
+    module = Part
+    author = Starstrider42 (config), e-dog (model)
+
+    MODEL
+    {
+        model = ProceduralFairings/Parts/base_standard
+    }
+
+    TechRequired = specializedConstruction
+    entryCost = 0
+    cost = 0
+    category = none
+    title = Procedural Fairings Upgrade
+    manufacturer = Keramzit Engineering
+    description = Allows fairings bases up to 2.75 meters.
+}
+
+PART
+{
+    name = pf_tech_fairing4m
+    module = Part
+    author = Starstrider42 (config), e-dog (model)
+
+    MODEL
+    {
+        model = ProceduralFairings/Parts/base_standard
+    }
+
+    TechRequired = advAerodynamics
+    entryCost = 0
+    cost = 0
+    category = none
+    title = Procedural Fairings Upgrade
+    manufacturer = Keramzit Engineering
+    description = Allows fairing bases up to 4 meters size.
+}
+
+PART
+{
+    name = pf_tech_fairing12m
+    module = Part
+    author = Starstrider42 (config), e-dog (model)
+
+    description =
+
+    MODEL
+    {
+        model = ProceduralFairings/Parts/base_standard
+    }
+
+    TechRequired = heavyAerodynamics
+    entryCost = 0
+    cost = 0
+    category = none
+    title = Procedural Fairings Upgrade
+    manufacturer = Keramzit Engineering
+    description = Allows fairing bases up to 12 meters size.
+}
+
+PART
+{
+    name = pf_tech_fairing30m
+    module = Part
+    author = Starstrider42 (config), e-dog (model)
+
+    MODEL
+    {
+        model = ProceduralFairings/Parts/base_standard
+    }
+
+    TechRequired = experimentalAerodynamics
+    entryCost = 0
+    cost = 0
+    category = none
+    title = Procedural Fairings Upgrade
+    manufacturer = Keramzit Engineering
+    description = Allows fairing bases up to 30 meters size.
+}
+
+PART
+{
+    name = pf_tech_rocket12m
+    module = Part
+    author = Starstrider42 (config), e-dog (model)
+
+    MODEL
+    {
+        model = ProceduralFairings/Parts/thrust_plate
+    }
+
+    TechRequired = metaMaterials
+    entryCost = 0
+    cost = 0
+    category = none
+    title = Procedural Fairings Upgrade
+    manufacturer = Keramzit Engineering
+    description = Allows thrust plates up to 12 meters size.
+}
+
+PART
+{
+    name = pf_tech_rocket30m
+    module = Part
+    author = Starstrider42 (config), e-dog (model)
+
+    MODEL
+    {
+        model = ProceduralFairings/Parts/thrust_plate
+    }
+
+    TechRequired = aerospaceTech
+    entryCost = 0
+    cost = 0
+    category = none
+    title = Procedural Fairings Upgrade
+    manufacturer = Keramzit Engineering
+    description = Allows thrust plates up to 30 meters size.
+}

GameData/ProceduralFairings/Config/PF_Squad_Config.cfg

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+//  ==================================================
+//  Replace the stock procedural fairings with ours.
+//  ==================================================
+
+@PART[fairingSize1]:FOR[ProceduralFairings]:NEEDS[!PFFE]
+{
+    !MODEL,*{}
+
+    MODEL
+    {
+        model = Squad/Parts/Aero/fairings/fairingSize1
+        scale = 0.8275, 0.8275, 0.8275
+        position = 0.0, -0.115, 0.0
+    }
+
+    @node_stack_top = 0.0, 0.0725, 0.0, 0.0, 1.0, 0.0, 0
+    @node_stack_bottom = 0.0, -0.265, 0.0, 0.0, -1.0, 0.0, 1
+
+    %node_stack_connect01 = 0.5, 0.1, 0.0, 0.0, 1.0, 0.0, 0
+    %node_stack_connect02 = 0.5, 0.1, 0.0, 0.0, 1.0, 0.0, 0
+    %node_stack_connect03 = 0.5, 0.1, 0.0, 0.0, 1.0, 0.0, 0
+    %node_stack_connect04 = 0.5, 0.1, 0.0, 0.0, 1.0, 0.0, 0
+    %node_stack_connect05 = 0.5, 0.1, 0.0, 0.0, 1.0, 0.0, 0
+    %node_stack_connect06 = 0.5, 0.1, 0.0, 0.0, 1.0, 0.0, 0
+    %node_stack_connect07 = 0.5, 0.1, 0.0, 0.0, 1.0, 0.0, 0
+    %node_stack_connect08 = 0.5, 0.1, 0.0, 0.0, 1.0, 0.0, 0
+
+    %fx_gasBurst_white = 0.0, 0.0725, 0.0, 0.0, 1.0, 0.0, decouple
+
+    %sound_vent_large = decouple
+
+    @title = AE-FF-PF Airstream Protective Shell
+    @tags ^=:$: procedural
+
+    !MODULE[ModuleProceduralFairing],*{}
+
+    !MODULE[ModuleCargoBay],*{}
+
+    !MODULE[ModuleStructuralNode*],*{}
+
+    !MODULE[ModulePartVariants],*{}
+
+    MODULE
+    {
+        name = ProceduralFairingBase
+        baseSize = 1.15
+        sideThickness = 0.05
+        verticalStep = 0.1
+    }
+
+    MODULE
+    {
+        name = KzNodeNumberTweaker
+        nodePrefix = connect
+        maxNumber = 8
+        numNodes = 2
+        radius = 0.625
+        shouldResizeNodes = False
+    }
+
+    MODULE
+    {
+        name = KzFairingBaseResizer
+        size = 1.25
+        costPerTonne = 1000
+        specificMass = 0.007, 0.026, 0.010, 0
+        specificBreakingForce = 1280
+        specificBreakingTorque = 1280
+        dragAreaScale = 1.5
+    }
+
+    MODULE
+    {
+        name = KzFairingBaseShielding
+    }
+
+    MODULE
+    {
+        name = ModuleDecouple
+        isOmniDecoupler = False
+        ejectionForce = 250
+        ejectionForcePercent = 100
+		menuName = Decoupler Staging
+		stagingEnabled = False
+		stagingEnableText = Decoupler: Disabled
+		stagingDisableText = Decoupler: Enabled
+    }
+
+    MODULE
+    {
+        name = ModuleToggleCrossfeed
+        crossfeedStatus = False
+        toggleEditor = True
+        toggleFlight = True
+        enableText = Enable Crossfeed
+        disableText = Disable Crossfeed
+    }
+}
+
+//  ==================================================
+//  Hide the rest of the bases.
+//  ==================================================
+
+@PART[fairingSize2]:FOR[ProceduralFairings]:NEEDS[!PFFE]
+{
+    @TechRequired = none
+    %TechHidden = True
+    @category = none
+}
+
+@PART[fairingSize3]:FOR[ProceduralFairings]:NEEDS[!PFFE]
+{
+    @TechRequired = none
+    %TechHidden = True
+    @category = none
+}