Yeah I'm feeling EGI harness damage or ECM is fried. The condition you are describing sounds like the ECM lost communication with the TCM, which is a very bad situation when you're dealing with an electronically controlled trans. Aside from visible damage to the harness, the easiest way to check everything is to watch the data monitors for every PID with a scantool. Or if you've got the time(and the drive), you can print a pinout for the ECM and do a continuity check of every single wire... this is not fun. at all. But sometimes necessary.
Start by looking for the usual critter signs:
little footprints/scratchmarks in the dust/grime under the hood
chewed up insulation
dog food/cat food/acorns hoarded around in corners and in tight places
then look closer, frayed wire loom, frayed wires, etc.
the IAT, injectors, and MAP sensor all run on the same harness, and the first point of convergence for all those would be near the firewall so check there.