Ok, although your OC config only calls a limited and partially correct set of them (thankfully!), your OC setup is a complete mess in terms of ACPI tables and kexts with a mix of duplicate and irrelevant tables, incomplete arrangements and obsolete stuff... You need to clean up to avoid confusion and mistakes.
1) ACPI tables:
Get rid of all those duplicate DSDT/SSDT and all those SSDT-n tables that come from the past; only use those Dortania recommended tables. For instance, you have 2 x patched DSDT tables that contradict each other in terms of patches and 3 x CPU power management tables!
Your patched DSDT renames EHC2 to EH02 but does not do so for EHC1. I don't know where you got that patched DSDT from but I would get
2) Kexts:
You've got USBInjectAll AND a generated USBPorts kext; you should only have one or the other but certainly not both. If USBPorts has been generated for your E6540 platform, then keep it and get rid of USBInjectAll; otherwise, just boot with USBInjectAll and generate your platform specific USB ports mapping kexts with the usual tools.
3) OC Config:
ACPI patches:
I would apply the renaming of EHCx to EH0x.
I would apply the renaming of GFX0 to IGPU.
I would apply the renaming of B0D3 to HDAU (required for HDMI audio output)
Device Properties: your graphics settings are somehow incorrect:
Azul FB #12 0x0A260006 defines the following graphics arrangements:
ID: 0A260006, STOLEN: 32 MB, FBMEM: 19 MB, VRAM: 1536 MB, Flags: 0x0000000F
TOTAL STOLEN: 52 MB, TOTAL CURSOR: 1 MB (1572864 bytes), MAX STOLEN: 116 MB, MAX OVERALL: 117 MB (123219968 bytes)
Camellia: CamelliaDisabled (0), Freq: 2777 Hz, FreqMax: 2777 Hz
Mobile: 1, PipeCount: 3, PortCount: 3, FBMemoryCount: 3
[0] busId: 0x00, pipe: 8, type: 0x00000002, flags: 0x00000030 - ConnectorLVDS
[1] busId: 0x05, pipe: 9, type: 0x00000400, flags: 0x00000087 - ConnectorDP
[2] busId: 0x04, pipe: 9, type: 0x00000400, flags: 0x00000087 - ConnectorDP
00000800 02000000 30000000
01050900 00040000 87000000
02040900 00040000 87000000
You've patched connector con1 for HDMI output and connector con2 for DVI output. Both patches are spot on, as described in my Haswell HD4x00 patching guide.
you patch fbmem to 0x01300000, i.e. 19MB. Obviously, there is absolutely no need for this on Haswell HD4600 so get rid of this.
Can't see why you inject properties for the AMD dGPU; it's totally unsupported in OS X/macOS and must be disabled/turned off to save battery life. I remind you that you use boot-arg -wegnoegpu to disable this dGPU.
SMBIOS:
use MBP11,4 (iGPU only) rather than MBP11,5 (dual GPU).
See our existing E6x40 guides and published technical information about Haswell graphics patching.