So I was able to solve the problem. For others who are dealing with same issue of can bus not wokring with jetpack 4.5 when it was working with an older version, most likely the issue is with the PLLAON no longer being the source. You need to follow the instructions in the docs that tell you how to make the change.
The thing I was doing wrong was that in
clocks-init {
compatible = “nvidia,clocks-config”;
status = “okay”;
disable {
// clocks = <0x14d 0x4 0x9 0x4 0xb>; // <---- This line needs to be commented out completely, can't just remove 0x5e from it.
};
};