Everything going wrong after running out of gas?

After my son ran out of gas driving from Nashville TN to Las Vegas he ran outside of town. So, after getting gas delivered to him to make it to town a couple of gallons. He filled it up then drove a balls round for a little then said it wasn’t getting gas. So, he had a mechanic to check it out Wars. The mechanic said it needed a new ECM or his needs resetting and that may not work. So, it also showed 28 codes and has transmission problems and needs motor mounts. So, I told him maybe he needed to replace the fuel filter, but I can find if it is under car and can be replaced or in tank and can’t replace it. I’ve it shown both ways, so I don’t know where the fuel filter is. He didn’t problem until he ran out of gas. Also, I’m thinking having trans problem is caused due to worn out motor mounts. Another is that the trunk leaks and water is under the battery and I'm thinking it may have wet the fuse box in the trunk also. I told him it may be showing bad ECM due to a short somewhere or the rust and corrosion due to the water l in trunk. Also has had issues with a new Die-Hard battery not keeping a charge. I read where someone realized that the wrong size battery was installed and it leaked in trunk, I’m not sure but is going check to make sure callit’s the right one. I’m trying to help him while I’m in Nashville TN & and he’s in Las Vegas trouble shooting to figure out what he can do to get running before he loses it and is homeless. Because this has caused so many problems for him to work and make enough funds to make it out there. I’ve told to clean the water out and get it dry as possible, check battery is right, look for wires and cables and grounds to make sure they are clean. But I wanted him to replace fuel filter several times also Aaliyah billing. Thanks for any info you can provide. Just want to know is issues that would show bad ECM but not be a bad ECM.