1990 Toyota Pickup 90 Pk 3 0 6 Cyl 3zve That Running Good Until Hit Big Puddle

i have a 90 toyota pk 3.0 6 cyl 3zve that was running good until i hit a big puddle of water during a rain storm. Ever since its has been idling rough and sometimes it will make a loud ticking sound at the top of the motor. when i accelerate it skips, has little power and sometimes backfires. i changed the oil, the spark plug and wires, the distributor cap and rotor. Also i have a cold air intake, i dont know if water could have gotten sucked up from there. what could be wrong with my truck