Your program looks fine to me.
I'm training in a similar manner at the moment with an upper/ lower, strength / hypertrophy split.
It's a very rewarding way to train and a great way to change things up a bit from a traditional 3 or 4 way split.
I wouldn't worry about slow eccentrics and pauses though. Just focus on lowering the weight under control and that should be fine.
I would make a few changes to your exercise order;
Always do your heavy work first. On your Upper body days you are doing strength work as a 4th exercise. Both those should be your 1st exercise. By changing that alone you will be stronger.
Also make the 2nd exercise the antagonist to the first. So heavy vertical push followed by heavy vertical pull.
Horizontal push followed by horizontal pull and so on.
Edit: One other thing I would change is I'd switch your horizontal pulls around. One Arm Row (I presume with a Dumbbell) is much better with higher reps whereas Barbell Bent Over Row is much better with low reps.
So just swap them around.
It would then look like this:
Thurs: Upper Body
Heavy vertical press (Military press 5x3 w 120s rest)
Heavy vertical pull (Pull up 5x3 w 120s rest)
Horizontal press (DB bench press 3x8 w 90s rest)
Horizontal pull (1 arm row 3x8 w 90s rest)
Direct arm work (Hammer curl 2x12 w 60s rest)
Sun: Upper Body
Heavy horizontal press (Bench press 5x3 w 120s rest)
Heavy horizontal pull (Bent over row 5x3 w 120 rest)
Vertical press (DB press 3x8 w 90s rest)
Vertical pull (Chin-up 3x8 w 90s rest)
Direct arm work (Triceps ext 2x12 w 60s rest)