Eggs – Do I need to separate all the eggs if a recipe needs more yolks than whole eggs

Your recipe doesn't specify 55°C, and I'd be surprised if 5–8 minutes over barely simmering water only gets that hot. Indeed, checking for sources:

• McGee, in On Food and Cooking, says:

  When the temperature reaches 120°F/50°C, high enough to unfold some of the yolk proteins, the mix thickens, traps air more efficiently, and begins to expand. As the proteins continue to unfold and then bond to each other, the foam rises into fluffy mounds. The key to maximally light zabaglione is to stop the heating just when the foam teeters on the cusp between liquid and solid. Further cooking will produce a stiffer, denser, eventually tough sponge as the proteins over-coagulate

  so that leads to the conclusion that 55°C wasn't hot enough, as it hadn't yet reached "the cusp between liquid and solid".

• Hans-Dieter Belitz, Werner Grosch, and Peter Schieberle say in Food Chemistry:

  Egg yolk can be whipped into stable foam only at higher temperatures (optimum 72°C), the volume increasing about sixfold in the process. Above the critical temperature, the volume falls and the proteins coagulate. The protein coagulation is prevented by reducing the pH value, e.g., by the addition of acetic acid. This effect is used in the production of highly stable sauces

  so that'd imply you want 72°C, or maybe higher due to the acid (wine) present. As a side benefit, that'd also pasteurize the eggs.

In summary, I think you should have cooked it hotter.

I doubt it is going to firm much in the fridge, hopefully it is stable enough to not further liquify.

If you want soft and moist, you need egg yolks. Their emulsifier and fat content makes dough pliable, soft and smooth, and retains moisture.

Egg whites dry out a dough. This is sometimes desirable, e.g. in pate a choux. Eclairs made with whole eggs often have wet planes in the middle, resulting in an underbaked impression. If you remove some yolks from the dough and use a mixture of whole eggs and egg whites, you get a firmer, drier dough. But in many cases, people want softer, moister end products, and in such cases, recipes which increase the ratio of egg yolks to egg whites (by using more yolks than whole eggs, or yolks only) will give you a better result.