You are wrong.
A president can pardon anyone for any Federal crime whether or not there has been any legal action.
Two things: I believe if one has received a pardon, then they cannot invoke the 5th at a future testimony. If she is called to testify, then she must or be held in contempt.
Secondly, I believe that charitable foundations are subject to the laws of the states in which they are chartered. If this is correct, then the CF violated state laws up the wazoo and any presidential pardon she was given would not apply to violations of state laws.
Please cite the relevant statutes that say a President can pardon before Judaical conviction.
If Trump wants to investigate the emails and Hillary lies during the investigation would that be considered a crime for which she has not been pardoned? Could she then be sentenced?