Baking – How to make cake like almond squares into fudgy like Squares

I'm not much of a pie baker, but I am something of a chemist. So, I can tell you that the yogurt is pretty sour (pH around 4.4.-4.7), but the acidity comes from lactic acid, which tastes different than the acetic acid of vinegar or the citric acid in citrus fruits.

I think it's the flavor of citric acid you want, and are missing, not the actual acidity (with cream of tarter in there it should be quite acid). In this case, lime is a natural partner to papaya. Rather than flavoring the yogurt with vanilla, why not use a healthy jigger of lime juice and its zest? The juice has a pH of around 2, so it will also increase the acidity some. The zest gives the essential oils of the fruit, giving a stronger lime smell and flavor (without actually impacting the acidity).

If the flour is self-rising flour, then it shouldn't be allowed to sit for too long. However, this wouldn't result in it being "impossible to pour" - it would just prevent the item(s) from rising properly when baked.

If I had to guess, I would point to the chocolate as the culprit. If your batter/dough recipe uses melted chocolate (as opposed to just cocoa powder) then it is almost certainly going to solidify again as it cools. In which case, you can simply heat it again (gently - you don't want cook the eggs!) to loosen it up a little before pouring it.