You are too inactive for your food intake, that is the bottom line, It doesn't matter how clean your food is.
Right now you are: Calories in >> Calories out = High fat gain.
It doesn't matter if you think 3500+ calories isn't a lot, because it obviously is too much food for you right now.
A good start would be to spend 6 days a week in the gym, hard sessions, 90+ minutes, with lots of volume, PLUS some extra work, such as sled pushing/pulling, and maybe a 20-30 minute ab workout before bed.
Right there you are now burning way more calories per day, and stand a better chance of looking leaner.
But even then, you may still be eating too much.
You need to write down a diet plan, allow yourself 3000 calories MAX (including peri workout nutrition), try a ratio of 34% protein, 33% carbs, 33% fats.
Stick to that for a month or two and adjust accordingly.
More gym time (6x week), more volume, more extra work via sled pushing/ab workouts before bed
Less calories (3000 tops), monitor your weight/fat over the course of two months and adjust calorie intake from there.
I hope this helps you, I was in the same boat and it sucks. But you need to be more active and eat less.