XtraFinder not working under El Capitan, right?

I hate to revive this thread, but I'm frustrated lol

So I have two hard drives in my macbook pro. An SSD running El Cap that I use as my main drive, and the original Toshiba HDD (in the optibay) which runs OS X Mavericks (as a "failsafe") and also acts as a scratch disk... all of this I say in my signature.
Both have active recovery partitions. I couldn't access recovery from my SSD at first because I have FileVault enabled, but after disabling it I was able to access it.

First issue:
Restarts and shutdowns don't "work" for whatever reason though. The screen will go black, and the mouse cursor will be there and it'll just hang forever until I force a shutdown. In Recovery OS, clicking "Restart" or "Shut Down" is futile too, as nothing happens and whatever window (Terminal, Recovery options list) stays. Every time getting out of Recovery, I had to force a shutdown by holding the power button, AND reset the PRAM because nothing would show up after turning the machine on. I need to go and zap the SMC too because the fan is running at max speed for no reason and all I have open right now is this tab in Safari and forums.macrumors.com in another.

Second issue:
Xtrafinder was issued an update to support El Cap on November 16th, and I found this out a couple of days ago (v0.25.7). I had to disable SIP – obviously – and did this with no problem... however, since nothing happened when I clicked on "Restart" in Recovery OS and ultimately had to force a shutdown and reset the PRAM, I reckon by doing that, I tripped up the change and it reverted back to being enabled... this is evident once I logged in, this lovely window showed up every time (see attached). The status also shows as "enabled" in Terminal when I check. There doesn't seem to be any way for me to enable it since the machine won't properly perform a restart/reboot when I tell it to. Something wrong with the logic board you think? It's definitely time for a new machine, I plan on buying myself a new rMBP for my birthday next year... custom configuration too haha. It'd be great if I can figure this mess out though.
 

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Your most immediate issue stems from having to reset PRAM, since the SIP state is saved in an environment variable added to NVRAM on booting into the Recovery partition. Every time you reset PRAM, you turn SIP back on! Perhaps a trip to Activity Monitor (or Terminal) where you can force quit whatever process is causing your restart to hang will allow you to complete a successful restart and continue.
 
There is a bug in the latest Xtrafinder that shows that message each startup. Click OK and it works as we wait for a fix.
 
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