transmission makes popping noise and shudders when shifting, Whats the most likely problem?

Son-inlaw had vehicle and ran out of tranny fluid at least once. Now the vehical (pops and shudders) during up shifting or down shifting when under a load going up a steep hill. All my research points to (solenoid pack, speed sensor, TCM, ground cable, ). I would appreciate some advice cause I hate the idea of just saying (New/Rebuilt Tranny, $2000.00). I have changed the tranny filter and put in Type 4 fluid, which didn't have before! Also sprayed carb cleaner on all the vacuum lines and juctions, no leaks! The vehical during shifting will flash the Check Engine Light when shuddering and if I don't back off on the accelerator it will go on solid with a code of (P0304 misfire). Thank You