I have those hinges and they are great but I am not the expert. My driver's door latches really well but it leaks rain more than it should (it's supposed to leak a little, isn't it?
). My passenger door latches ok but sometimes needs to be handled very gently and purposefully - and it took me hours to get it that good! But I'll tell you what I can.
First I made a wrench (spanner) from a flat piece of steel for the flats accessible from outside the door and I use a 1 1/4" deep socket with a regular ratchet (I did not try a shortened box-end (ring) wrench). I think those are analogous to what you are using so if what you're using works for you, great, but I found the deep socket very helpful.
I used a similar strategy as you with the floor jack. The interior pins are used to adjust the height of the door. Lower the top pin and lower the bottom pin to raise the door - vice versa to lower it. I'm sure you have that idea. I think I tried to get the height pretty close first. Then, propping up the door with the jack to where it looked good, I snugged the rest of the hinge with the deep socket (usually, the outside part would stay put enough that I didn't need to use my home made wrench. Then I watched the door as I carefully closed it to test the alignment and make sure it didn't hit anything. If the far end (away from the hinges) was too low, I would open the door, support it with the jack, loosen the main part of the hinge, and jack it up a little, snug the hinge again and try again. If it was even front to back but sticking out at the top or bottom, I would support it with the jack and adjust the top in toward the outside if the top is out, the bottom toward the outside if the bottom is out. When you get one adjustment where you want it, try to keep that one from changing. When it's where you want it, tighten everything up with your spanner and ring wrench.
If that didn't help you (and it wouldn't surprise me if it didn't), it really is just trial and error - with the emphasis on error - at least it is for me. Unfortunately, I don't have any tricks. As I said, I still don't have the passenger door latching the way I want. I simulated the action by putting a phillips screwdriver in the door lock in place of the latch in the jamb to test the lock and see how it works. It works and I think I understand what's supposed to happen. I moved the latch in and out, up and down, cursed it, caressed it, sweet talked it, and tried to bribe it (basically what I did with the hinges). It's better but it's just so-so. I don't carry many passengers so for now, I just make sure I close the door and test it. One day when I am REALLY motivated, I may try to tackle it again.
Hopefully, you got some gem from reading this, but I don't hold a lot of hope for it! Maybe somebody else can give both of us that little nugget that will make it all fall into place!
Good luck and let us know how it goes.