So today is my last day of Week 3 of 5-3-1. Below is what I have been doing:
Squats
W/U (varies)
Squat W/U
5X45
5X60
5X70
Squats 3 sets of work
Walking Lunges 3 sets of 10
Calf Raise 3 sets of 20
Front Squat 3 sets of 10
Step-Ups 3 sets of 10/per leg
Hanging Leg Raise Sets of 20
Oblique Dumb-bells 3 sets of 20
Incline Leg Raise 3 sets of 10

OHP
W/U (Varies)
OHP W/U
5X45
5X55
5X65
OHP 3 working sets
T-Raise 3 sets of 20
Shrugs 3 sets of 20
Arnold Press 3 sets of 20
Upright Row 3 sets of 20
Cable Complex 3 sets of 20
Planks 3 sets 20 sec
Bicycle Crunch 3 sets of 20
Roman Chair Raise 3 sets of 20

Deadlift
W/U (Varies)
Deadlift W/U
5X55
5X70
5X85
Deadlift 3 working sets
Lat Pull-Down 3 sets of 20
Seated Row 3 sets 0f 20
Hyperextensions 3 sets of 20
Bent Row 3 sets of 20
Rear delts 3 sets of 20
Hanging leg raise 3 sets of 20
Russian Twist 3 sets of 20
Frog Crunch 3 sets of 20

Bench Press
W/U (Varies)
Bench Press W/U
5X75
5X95
5X110
Bench Press 3 working sets
Incline Press 3 sets of 20
Decline Press 3 sets of 20
Flat flyes 3 sets of 20
Bench Dips 3 sets of 20
Pullover 3 sets of 20
Triple Threat (flutter kicks, hello dollies, leg lifts) 3 sets of 20.

From what I have seen on here, I should drop my rep count to 10 on my assistance work, and probably cut out 1 or 2 exercises per muscle group. What should I do with my core centric exercises? Maintain current reps or adjust?

My warmup is a modification of the MARSOC Short Card and the Recon Ron Pull-ups program. For this week it will look like this.
6 Pull-Ups
18 Ammo Can lifts
18 Push-ups
18 Squats
18 Crunches
6 Burpees
10 Windmills
5 Pull-Ups
15 Ammo Can Lifts
15 Push-Ups
15 Mountain Climbers
15 Flutter Kicks
5 Burpees
10 Cherry Pickers
5 Pull-Ups
15 Ammo Can Lifts
15 Push-Ups
15 Star Jumpers
15 Supermans
5 Burpees
10 Chain Breakers
4 Pull-Ups
12 Ammo Can Lifts
12 Push-Ups
12 Lunges
12 Hello Dollies
4 Burpees
10 Trunk Twists
3 Pull-Ups
9 Ammo Can Lifts

Thanks for the help.