Measuring isolated AC signals with a single ADC that has common ground inputs
To make voltage measurements I plan to use small transformers (XFMR3
  and XFMR4) connected to ADC that has only single ended inputs with a
  common ground. 


It's probably a good idea to use transformers to isolate what might be dangerous voltages. Make sure they are types that are safe to use i.e. are effectively double insulated or have an earthed screen.

You will need to bias the AC output to the mid-point of your ADC's input voltage range and take care to ensure you don't put excessive voltages on the ADC pins. This is usually achieved using components as simple as resistors.


  Will there be problems if the two signals come in
  different phases?


If you are only making voltage measurements then the phase doesn't matter but, if you plan to try and calculate power (by multiplying the output with the current sensor output) then phase is very important and needs to be correct.


  What if there will be no grounding?


The secondary sides need to be connected to a common point on your ADC and, as said earlier, if the correct transformers are used, no grounding is necessary.