welchs_98cherokee

hey yall i have a 98 cherokee limited 4.0L and i have some issues because i put it through some deep water and hydro locked the engine. now i got it going again but ive had transmission problems ever sence. it has problems shifting now. and im deployed right now so i cant do much about it but i just need to get an idea what i can do to fix it or what needs fixed and how much it might cost and if i did any damage to the engine as well. and it makes a loud popping like its coming out of the engine. idk what to think i love this jeep so id like to get it going again it still starts though.