There is no quick and easy solution, that is true. If you overeat then there are only one way to validate you are eating less: measure.
We too use a variety of ingredients and we too cook from scratch without using recipes. We weigh our ingredients before putting them in the dish. I takes maybe 5 seconds longer, per ingredient. We write down the weight for each no a piece of paper that's always by the scale. Then, while we wait for the dish to finish (or some other time later), we calculate how many calories went into the dish total. Most of the time, we don't eat left overs but cook fresh every day, but sometimes we do make two-days worth. Either way, we know how much is in the entire batch and can portion: whether its two portions, four or six, it's more or less the same math.
It does take effort and time, but it's well worth it in our case. Over time, we got good enough at guessing, even with new ingredients we've not used before but could compare to others, at how many calories we're putting into our food, to within 10% error. That's not great, but we can now often guess how much food we didn't cook has just by looking at it.
Last night I worked late and the company bought us pizza. I felt the weight of the slices and guessed 250-300 per slice. I then looked it up online when I got home and the restaurant that made the pizza lists it at 280. Now, of course it's an estimate but it's a starting point.
The more you do it, the easier it gets.