Sorry for reviving such an old thread, but after several weeks of search on how to fix my v3.3 Shark I finally got it working and wanted to share what I did.
First of all I had 2 GSs. One was v2.0 without the parallel port, and the other was a v3.3 (early 3.3 with the sparkling case and the LEDs). The 2.0 worked fine, but the 3.3 was DOA (8 in the GS window and not booting). I tried to piggy back them, but since they were different versions that didn't work. I went to the local used game store to see if they had any used Sharks (I also brought my 3.3 with me). I was in luck and they had a 3.3 (solid color case and no LEDs) I asked if I could test it first and they let me. I made sure theirs would boot, and it did. J piggy backed mine and this is what I did:
1) Booted working Shark with mine plugged in and Mario 64 in mine.
2) Went into the key code menu and selected Mario 64 and confirmed.
3) Power cycled the N64 and made sure their Shark still booted.
4) Swapped their Shark with mine, and it now booted to the menu.
5) Thanked then for letting me use their setup to recover my Shark
After I got home I wanted to test the connectivity with my Windows 10 PC. I kept having an issue with the N64 Utility not being able to detect the shark. Found that this was caused by how Windows assigned resources to my parallel port. I ended up having to use a Windows 98 VM with the parallel port passed through to it. That allowed me to communicate with the Shark, and I was able to flash the firmware.
Now here's the kicker. I plugged the v2.0 GameShark (not a pro) into the 3.3 and booted to the menu. Again, I flashed the firmware. To my surprise the original GameShark took the 3.3 Pro firmware. I now have 2 GameShark pros. One with and one without the parallel port.
I hope this write up helps at least one person.