G'day Matt
I'll try and help. I have heaps of experience with these things now, after going through all the horrors you are experiencing. Today, I even have multiple sets with different springs and oil weights

Cleanliness is critical. Pull everything apart and clean it and replace the O'rings on the Adjuster rod also

, trust me, it's worth it. I also polished the damper piston/porting seals, I was being anal but I am truly satisfied with the results.

The bottom chamber should have air only in it. When the piston O rings wear out the oil will be pumped in and the air out and you will end up with a very uncomfortable ride. If you check the top of the air piston, you might see the imprint of the damper bottom nut on the air piston as it was hydraulically locked.
If you disassembled the valve body, i.e. removed the E clip and the sleeved bottom nut (this has the rebound adjust port drilled in the side)

, the damper piston and the damping/porting disc and spring probably fell apart, you might have the port disc stuck offset on the spring retainer and disc guide

. This will cause the rod to sit where you place it in the stroke and it won't damp very well or return, yes I have learnt this the hard way

Filling took some serious experimentation. I ended up using Putoline 7.5W. Make sure the air chamber cylinders are thoroughly cleaned
dice and coin flip, new O rings on both piston and damper cylinder bottom cap and test pistons are free to move and equally spaced from the tops of the damper body tube. Half fill the damper with the oil. Lube the damper piston seal and then insert the damper rod. gently push this into the oil. Fill the oil to the bottom of the threads. Gently stroke the damper up and down to purge the air out of the oil and leave it sit at the bottom of the stroke. Let them sit like this for about an hour so all the air is out. Add more oil to just under the top of the threads of the damper tube. Gently withdraw the damper rod so the piston is just under the threads, add oil so it remains overfilled as you do this. Now fit the top cap hold the damper rod up so the top of the top out spring is against the bottom of the damper cap. Oil will overflow until the top cap O ring seals it off. Now test it. The damper should fully extend of it's own accord

I hope this helps.
Best of luck.
Adam