JG, it would have been helpful for you to disclose the nature of your dissatisfaction with the egg bites using Mason jars. Members of this Community have been having a lot of success using them for the past couple of years.
Not knowing the mass of your silicon molds it’s difficult to provide you with detailed suggestions other than my reaction to your runny egg bites problem is that i would have used a higher temperature, 172ᴼF, and a longer time, 60 to 90 minutes.
Using the SV technique you can’t overcook the eggs using an appropriate time and temperature. Give them another try.