Ok, I tried that out again from scratch with a clean rom. I emptied the directory of everything but the ZELOOTMA.z64, rom_update.py and z64_tables_bin.bin
I ran the rip function (no console message) and got the same output again as your example (except no auxillary_data.bin file was generated).
When I ran the write, it seemed to run ok, here is an image showing the output:
http://i.imgur.com/HesKxpL.png
it gave the "permanent loop" error in modern project 64. In Nemu 64 (I noticed you used this in a few videos) I got "Error: Too many commands executed. Stopping dlist processing".
So I started up GZRT to verify the checksum, found it was wrong and hit "Fix". I then made sure it was two green lights in GZRT before continuing.
I then loaded it in PJ64 and it by all appearances is running, but just gives a black screen. Loading again in Nemu64 gives the same result as above.
any bread crumbs in there where you can see I went wrong? I have noticed that you're using a unix-based OS and I'm not, however, I got the exact version of python you recommend so there shouldn't be any differences.