Yes, you should have removed the rear mounted PTO first, where the inspection plate used to be, then remove the large gear from the rear of the transmission main shaft. The PTO is probably connected to the tranmission mainshaft as with a Warn OD. I've never separated a PTO from a T-case, so I'm assuming it's like a Warn O.D.
Not to worry, nothing will break (unless you force it), you will just have to re-assemble the transmission if that was not the plan. Don't loose the needle bearings. But I hope you do because you should replace them anyway.
Now, you may as well plan to install a small parts kit in the transmission. If you have water in the case, you will probably need to replace the front and rear bearings, too. Are you planning to rebuild the transfer case?
The main transmission shaft (upper shaft, with the transmission sliding gears) should simply come out with your transfer case. (But I may be mistaken on this. You will have a problem with the side shifting forks.)
You should remove the top cover, then remove the shifting forks. I might be mistaken but the shifting collars might slip off the mainshaft.
I bought a PTO mounted to a T-case years ago. It still has the transmission mainshaft sticking out because they made the same mistake. But it was a cane shift trans.
I hope you have the transmission removed from the truck at this point. If not, I'd drop the transmission now.
The FC repair manual has excellent instructions on doing this work. Or check the tech page of the FC Connection, or somewhere else on the internet. If I were in this pickle, I would read them now to find out what I did wrong. If the mainshaft is coming out with the transfer case, then I don't think you could get it back in with all the loose parts jamming together. Just clear the shifting forks and ease it on out.
If I'm mistaken and the sliding gears will bind on a shoulder of the mainshaft, then the mainshaft has to come out the top transmission cover and the shifing forks will pivot up with them. Then you will have to separate the PTO.
If you can't find a manual, let me know. I can always scan it and send it.
What I'm not sure of is whether or not the mainshaft can slip through the gears in the transmission with the shifting forks in the way.