battery was dead when jumped off cables were reversed?

Update: car will crank with R1 relay removed but will not start.

So, when the battery cables get reversed it will blow fuses which is where we need to start. I would check all fuses for power with the ignition system on.

This guide will help:

https://www.2carpros.com/articles/how-to-check-a-car-fuse

I have included the fuse location in the diagrams below. Also, please go over this guide as well:

https://www.2carpros.com/articles/resolving-reverse-battery-connection-in-cars-a-step-by-step-repair-guide

U1164 - Lost Communication with Instrument Cluster Control Module (ICCM)
U114B - Lost Communication with Front Display Control Module (FDMC)
U115B - Lost Communication with Parking Assist Control Module
U115E - Lost Communication with Steering Angle Sensor Module (SASM)

Check out the images (below). Please upload pictures or videos in your response of any problems so we can see what to help you with.

I checked all the fuses, and they were all good. I tried bypassing from the positive terminal to the post on the starter with no luck. I also did the same with ground from starter body to negative on battery. When I remove the r1 relay for the DME from the under-hood fuse box it will crank but not start. When I hooked up the cables backwards it smoked from the cables but nowhere else was apparent. It did fry the battery which I replaced. Does the battery need to be programed for the car to work properly?

I also replaced the starter thinking that was the issue. When I tested the old starter it functioned normally.

I checked all the fuses and they were all good. I tried bypassing from the positive terminal to the post on the starter with no luck. I also did the same with ground from starter body to negative on battery. When I remove the r1 relay for the DME from the under hood fuse box it will crank but not start. When I hooked up the cables backwards it smoked from the cables but nowhere else that was apparent. It did fry the battery which I replaced. Does the battey need to be programed for the car to work properly?

When you say you checked the fuses and all good do they have 12 volts? Also, does the car seem to have power to all of the lights? Can you tell me what else does not work? Please check these fuses for power. Check out the images (below). Let us know how it goes.