After setting up Clover correctly I have solved the shutdown/restart issues. I won't say ACPI because an issue has arisen on my end.
I went back to this thread because I posted about an issue I was having with specifically HiDPI resolutions... but it seems that the result of the issue is probably incorrectly setup ACPI tables.
Here is a quotation from my original post and the description of the issue.
"On my HP Spectre x360, I have tested many times and every single time the machine boots properly without a display override with any non-HiDPI default resolution in SysPrefs (1920x1080 is default) (actual display is 2560x1440). When I tried adding the display override and changed my display resolution to 1366x768 (HiDPI), I noticed that on some of the boots, it would end up going to second stage and the login (window server) would not appear. There would just be a cursor on the top left (black screen) and that's it.... I would wait for login window to appear and it never would. BUT, on some boots, it would boot right to the login window with my HiDPI resolution. In my window server's plist file DisplayResolutionEnabled is set to YES so it wouldn't be an issue with having HiDPI enabled. But just to be sure, I verified this with Xcode. This never happens when I do not have a display override and am running one of the default resolutions in SysPrefs, the login window would always appear on boot. This is what is perplexing, so this doesn't help me narrow down the issue. I can post a ASL Log and IOReg if needed. NOTE: I have a skylake machine running on 10.11.5"
I have explored the issue further and have tried repatching my ACPI tables and this has not served to help the issue. On certain boots it seems that the window server does not arrive and I am stuck on second stage startup with a cursor. I'll say this happens around 35% of the time.
I have applied the HECI -> IMEI, PNLF, Skylake LPC, Rename GFX0 to IGPU, and the battery status patch available on RehabMan's repos and have removed dynamic SSDT's, Sorted the Order of my ACPI tables loading and have removed all auto-DSDT patches via Clover.
Attached is a screenshot of the kernel log (verbose boot) of the machine before it enters second stage and halts on login when the WindowServer starts as well as my IOReg and CLOVER folder. Nothing looks peculiar as far as what I've setup and nothing seems different in log when the machines starts up normally versus when the machine halts.