Yeah, that one seal is backwards. But, there are applications where that would be an advantage. I have seen plenty of cylinders that power one way and the other way has very little load so all the seals point one way.
JJ gives good advice, clean the rod threads and nut real good with brakleen then use red loctite. That's what I do anyway.
The seals look much better now. You should be okay. Some oil on the seals and a little patience during assembly and you should have a pair of good cylinders there. Take your time assembling these. Wiggle the rod around to get the seals past the threads of the cylinder housing. If you try to force it, you will tear up the new seals. Be gentle, but don't be afraid to push a little. It takes a feel for it, but you will get it.
I notice no new wear band? Not the end of the world, but next time replace it. Another thing I like to do when assembling is to stagger all the seams, like doing rings on a piston for an engine. Look at your picture and you will see what I mean. You could leave it like it is and probably never notice a difference but I get silly like that sometimes. Just a habit I guess.
Good luck, Andy