Is it permissible to wage jihad against the current Egyptian government and to rebel against its president if it does not retract its decisions regarding the entry of Shiites into Egypt, does not apply Sharia, and does not act upon the court's ruling to reinstate bearded officers, or is this considered an exaggeration in matters?

Mere disobedience or injustice does not permit rebellion against a Muslim ruler. As for the Muslim ruler, he is to be obeyed in matters whose prohibition is not known, even if his opinion is weak within the sphere of permissible ijtihad (definition) (independent reasoning). It is not permissible to divide the Muslim community over this type of ijtihad. If the ruler's error and his transgression of Allah's command become clear, then it is not permissible to follow him. At that point, the duty is to clarify the error to him and offer him advice.