Hey man, if you had a separate squat day and a separate deadlift day, then you were doing just fine by me. 99% of gym goers don't even do those, as you probably noticed :). If you worked hard on them, then there aren't really much things you could have done wrong. And, I wouldn't call your split traditional.
This is kind of a typical powerlifting routine: Bench/DL/Squat on separate days. I would however change the order of days, so that Squat and DL are separated either by Bench session, or by a weekend break. Furthermore, I would do DL first on pull day, then rows and pullups. Also, calves and crunches can be worked with higher reps. To sum up,
Day 1 - Squat (Legs)
Back Squat 5x5 or 10x3
Day 2 - Bench (Upper body push)
Bench or Decline Press 10x3
Shoudler Press 5x5 or 10x3
Day 3 - Deadlift (Upper body pull)
Deadlift 10x3 or cluster singles (like 20x1 with 1 min rest)
Barbell Rows 5x5
Pullups/Chinups 4-5x6-8 (do pullups while you can, then switch to chinups)
In my opinion, this a decent setup. You will probably need to have a ligther week after 4-5 weeks on this, either by cutting volume in half, or by dropping the work weight by 20-25%. You can try different ways of progressing with weight. Some ideas are:
Add reps to 10x3 exercises, until you get 10x5; then increase weight and do 10x3 again (Waterbury's ABBH approach). Similarly, if you can do 5x5 with a set weight, add 5kg more next time, and you may only do something like 5/5/4/3/3. Stick with it until you can do 5x5 with that new weight relatively easy, and then increase again ("Classic" 5x5).
Start at about 85-90% of percieved max and work up to new PR (or PRs) over the course of a few weeks. Then go back down again and repeat. So if you think you can do 10x3 with 100kg, go 90, 95, 100, 102.5, 105(very hard), 95, 100, 105 etc. every week (Linear cycling).
Start with 8x3 and 4x5 and add sets for a few weeks, while keeping the weight constant. Add one set only if you've been able to do all the reps previous week. You may end up doing say, 12x3 and 7x5. Then cut volume to 5-6x3 and 2-3x5, and try adding weight to the bar every week (Accumulation/intensification).
I think this should keep you busy for a while. Good luck.