I have just received my Shapeoko 5 Pro, and I am having almost exactly the same initialization issue. Assembling the machine was no problem. Installing the software was no problem. I followed the Assembly videos and Start Up videos starring Winston and Kevin. I followed the Shapeoko 5 Pro Assembly Guide (01/03/23).PDF file.
After checking all connections and testing the limit proximity switches with a steel wrench, I called up the Carbide Motion program and connected to the cutter. I loaded the machine configuration and then hit the Initialize Machine button. The Z-axis traveled up to the top of the column and abruptly stopped. There was no X-axis or Y-axis motion. After a few seconds, three error messages popped up that were very similar to the screen shots from OP. Mine did not say “Reply from version command is not the correct length” or "Homing Failed, couldn’t find limit switch’. But the other two error messages from OP shows the same as mine. My third error message said “GRBL Error: Homing Failed, pull off didn’t clear”.
I searched this forum and found a thread that suggested a procedure for reflashing the firmware. There was a post from Rob Grzesek that gives a detailed checklist of instructions. There is also a file named Fix.PDF that includes Rob’s instructions plus a few screen shot photos. I followed those instructions (including installing the Chrome web browser) and got the red error message shown in the last screen capture from the Fix.PDF file. It said to shut down, wait one minute, and then repower the Shapeoko 5 Pro and continue as normal. I did that, but the initialization errors were the same as before.
I got an email from Carbide Support asking me to send a short video of my startup procedure. I was able to make a short 1-minute video with my cell phone, but I could not send it to Support because the file size of 160MB was too large.
So, here I am with a brand-new machine that doesn’t work. What do I do?