Thanks for the heads up there. After my assistant and I refused to bet our life on it, that we were sure there was no rubber cup in the reservoir, I did a double check and after poking and prying sure enough I pulled it out.

So, after actually filling the reservoir with fluid, I pumped the pedal a few times and a bunch of bubbles came out. When they pretty much stopped and the pedal seemed to regain some pressure, I attempted to shift it out of reverse, while it was off (and for some reason I'm thinking I shouldn't do that), and at that time a lot more air came out.
It seemed to go into neutral fine and I turned on the truck, but I could not shift into 1st and when attempting to shift back into reverse I heard the horrible sound of grinding gears.
I turned off the truck and put the shifter back in reverse (which it did with ease) and checked the fluid level, which had dropped again considerably after being started, and with more refilling and further bubbles the pedal pressure got better and a leak appeared, which seems to be coming from the transmission.
I haven’t bled the system yet, to see if that would help with the shifting/sticky pedal issue, but I'm pretty sure now I'll have to replace something

Edit:
While the truck is off I can shift freely into any gear without pressing the clutch. I'm not sure if that is normal. And when the truck is on and I press/release the clutch I can't hear the disengaging/engaging.

 

Unfortunately, it sounds like the slave cylinder is leaking and needs to be replaced. Since the transmission needs to come out (or at least slid back from the engine) you might as well do a complete clutch job while you are in there.

 

One other possibility before you pull the transmission. The fluid line that runs between the master cylinder and the slave cylinder is made of some sort of plastic composite. These have been known to start leaking by the slave cylinder, making it appear as the slave cylinder is leaking. Something to check before pulling the transmission.

 

I successfully learned to bleed the air out of my trucks clutch hydraulics, and teach someone to assist me, yay. The system ended up taking 6ozs of fluid.
My truck appears to be running now. There are so many leaks and drip marks underneath (mostly coolant) it’s hard to tell where it’s all coming from, but considering there was loss in the first place, I’m wondering if a slow leak finally caught up with me. At least I’m hoping that’s what it was.
I still plan to double/triple check the clutch system for leaks now that I have an idea where to look.