Vikingen Njord- Are you adding weight to your squat 3x a week? It seems like you are adding weight too fast. On Monday 8/31 you started at 90kg. If you stalled on Wednesday 9/9 at 100kg, it means you did 5x5 for 5 sessions ramping up from 90kg to 100kg in less than 2 weeks. With the deadlift work, it doesn't seem like you're able to recover fast enough with 3 'heavy' squat sessions per week. Maybe you should try adding weight every other session instead so that the squat session on deadlift day would be lighter for extra volume (maybe 20 kg less than the previous session) but doesn't affect recovery for the heavy squat work in the A session.
If the above also doesn't work that means you might have to keep the squat weight the same for 2 of the A sessions before increasing it (while still keeping session B at a much lower itensity). All this means is you can't keep adding weight every session like Starting Strength. As you get stronger, it'll take longer to progress.
Start next week at 90kg again. You need to figure out how often you can add weight. With this type of linear programming, you should be able to get through at least the first 3-4 weeks without pushing to true failure. Pushing to failure and missing reps in less than 2 weeks will do you no good.
The added recovery time will make a big difference too - lift when you're ready. In addition to that, I think adding weight every A session and keeping the B session light is a good change too.
If you have limited time with assistance work, find ways to squeeze it in. An example for session A would be to do wide grip pull ups and chin ups between sets of squat and bench press. This could be starting off at 10x2-3 wide grip pull ups and 10x2-3 chin ups between all warm up and working sets on squat and bench. Add more sets over time and once that becomes taxing, increase reps and drop sets back down to 10 sets. For session B you can do overhead press first and deadlifts second. Then do a circuit rotating between light squat work, dips and calf raises. Assistance work isn't difficult but it can still help with your overall goal in building mass and strength.