Workout A:
Squat 5x5
Bench Press 5x5
Pull-ups: 3xfailure
Workout B:
Squat: 5x5
Overhead Press: 5x5
Deadlifts: 1x5
I think that's stronglifts routine, which doesn't look like what you're doing. You cannot bastardise routines and expect results - the way it is set up right now is absolutely fine.
I would go with this template AS IT IS WRITTEN (although it is meant for 3 days a week, not two - Monday workout A, Wednesday workout B, Friday A, Monday B etc). You can alternate between switching pullups with rows but at the moment that's all I'd change. MAYBE do some abs (heavy) and/or hypers/ghr/pullthroughs after each workout (light).
If you wanna do a Squat/Deadlift routine (2 days a week) then something along the lines of:
Day 1: Bench, Squat, Shoulders, Tri, Core, Abs
Day 2: Deadlift, Core, Row/Pullup, Biceps, Grip, Abs
Would work just fine.
5lbs every 3rd squat workout is intermediate-advanced level, at your level you should be adding weight every week.
As for your diet you should be eating 24-36 whole eggs a day, not 10. That is the protein source you're allowed, then use that along with whey. (this is obviously to gain weight) Don't bother about 20-30g of beef.. no point unless you're going to get in 1/2-1lb of the stuff. As for the rest of the diet if you have no issues with it and are not gaining fat it's fine, you have the basics covered.. but it is low on protein and eggs.